HELIOS Digital DAQ - User contributions [en]

Locations

2026-02-06T23:38:03Z

Ttang: /* Nat Box / Rounter */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

<s>The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)</s>

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC || accountName || onenetIP
|-
| DAQ || helios || digios1
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

{|class="wikitable"
! Computer || IP
|-
| IOCs || 192.168.1.2X
|-
| DAQ || 192.168.1.2
|-
|MAC2020 || 192.168.1.164
|-
|MAC2017 || 192.168.1.193
|-
|Windows XP || 192.168.1.191
|-
|DAQ power switch || 192.168.1.115
|-
|Terminal server || 192.168.1.3
|-
| HELIOS Mag Ctrl Pi || 192.168.1.208
|}

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

Locations

2025-06-27T16:54:59Z

Ttang: /* Nat Box / Rounter */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

<s>The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)</s>

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC || accountName || onenetIP
|-
| DAQ || helios || digios1
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

{|class="wikitable"
! Computer || IP
|-
| IOCs || 192.168.1.2X
|-
| DAQ || 192.168.1.2
|-
|MAC2020 || 192.168.1.164
|-
|MAC2017 || 192.168.1.193
|-
|Windows XP || 192.168.1.191
|-
|DAQ power switch || 192.168.1.115
|-
|Terminal server || 192.168.1.3
|}

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

Locations

2025-06-27T16:54:45Z

Ttang: /* Nat Box / Rounter */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

<s>The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)</s>

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC || accountName || onenetIP
|-
| DAQ || helios || digios1
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

{|class="wikitable"
! Computer || IP
|-
| IOCs || 192.168.1.2X
|-
| DAQ || 192.168.1.2
|-
|MAC2020 || 192.168.1.164
|-
|MAC2017 || 192.168.1.193
|-
|Windows XP || 192.168.1.191
|-
|DAQ power switch || 192.168.1.115
|-
|Terminal server || 192.168.1.3
|}

There are some unknown IP
192.168.1.3
192.168.1.81

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

Locations

2025-06-26T18:25:58Z

Ttang: /* Nat Box / Rounter */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

<s>The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)</s>

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC || accountName || onenetIP
|-
| DAQ || helios || digios1
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

{|class="wikitable"
! Computer || IP
|-
| IOCs || 192.168.1.2X
|-
| DAQ || 192.168.1.2
|-
|MAC2020 || 192.168.1.164
|-
|MAC2017 || 192.168.1.193
|-
|Windows XP || 192.168.1.191
|-
|DAQ power switch || 192.168.1.115
|}

There are some unknown IP
192.168.1.3
192.168.1.81

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

Locations

2025-06-26T18:19:17Z

Ttang: /* Login outside ANL */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

<s>The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)</s>

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC || accountName || onenetIP
|-
| DAQ || helios || digios1
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

IOC's are
192.168.1.2X
DAQ computer (digios1) is
192.168.1.2
MAC2020 computer (helios-iMac) is
192.168.1.164
Target Fan power switch (target-pwrswitch) is
192.168.1.106
DAQ power switch is
192.168.1.115

There are some unknown IP
192.168.1.3
192.168.1.81

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

Locations

2025-06-26T18:18:38Z

Ttang: /* Login outside ANL */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

<s>The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)</s>

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC ! accountName ! onenetIP
|-
| DAQ | helios | digios1
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

IOC's are
192.168.1.2X
DAQ computer (digios1) is
192.168.1.2
MAC2020 computer (helios-iMac) is
192.168.1.164
Target Fan power switch (target-pwrswitch) is
192.168.1.106
DAQ power switch is
192.168.1.115

There are some unknown IP
192.168.1.3
192.168.1.81

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

Locations

2025-06-26T18:18:09Z

Ttang: /* DAQ Computer */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

<s>The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)</s>

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC
! accountName
! onenetIP
|-
| DAQ
| helios
| digios1
|-
| Mac2017
| heliosdigios
| mac2017
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

IOC's are
192.168.1.2X
DAQ computer (digios1) is
192.168.1.2
MAC2020 computer (helios-iMac) is
192.168.1.164
Target Fan power switch (target-pwrswitch) is
192.168.1.106
DAQ power switch is
192.168.1.115

There are some unknown IP
192.168.1.3
192.168.1.81

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

File:Kinematics of HELIOS.pdf

2024-12-08T19:21:38Z

Ttang: Ttang uploaded a new version of File:Kinematics of HELIOS.pdf

Kinematics of HELIOS

File:Kinematics of HELIOS.pdf

2024-06-09T23:26:18Z

Ttang: Ttang uploaded a new version of File:Kinematics of HELIOS.pdf

Kinematics of HELIOS

Main Page

2024-01-09T20:55:19Z

Ttang: /* Hardware */

== HELIOS Digital DAQ Wiki Page ==

This is the wiki for all that is the [http://www.phy.anl.gov/atlas/helios HELIOS] Digital Data Acquisition (informally known as DigiOS).

For the kinematics of HELIOS, please look [[File:Kinematics of HELIOS.pdf|thumb]]

Online simulation is available [https://fsunuc.physics.fsu.edu/SOLARIS/ Here]

= Hardware =

{|class="wikitable"
!! Devices !! Function
|-
| Digitizers || digitizing analog signal
|-
| HELIOS DAQ || controlling and receiving data
|-
| Mac2020 || Remote control of the HELIOS DAQ and online analysis
|-
| Mac2017 || Database, Grafana, remote control of the WindowXP
|-
| WindowXP || HV control
|-
| HeliosDB (removed) || Database (replaced by Mac2017)
|}

Here are more detail

*:[[Hardware]]

*:[[Locations]]

*:[[Hardware/Firmware Configurations]]

*:[[VME99 test stand IOC]]

*:[[Target Fan Control]]

*:[[Detectors]]

*:[[Alpha source]]

*:[[PV List]]

= Software =

*:[[GUI, Scripts And Analysis Code]]

*:[[Data Storage]]

*:[[Input/Output Control]]

*:[[EPIC]]

*:[[gtReceiver + GEBSort]]

*:[[Grafana + InfluxDB]]

*:[[Globus]]

*:[[Leakage Current from Iseg]]

*:[[Ptolemy in Mac using docker]]

= Usage and Operation =

*:[[System usage]]

*:[[Sorting Data]]

*:[["How to" for DAQ]]

*:[["How to" for analysis code]]

= Others =

*:[[Experiments]]

*:[[System testing]]

*:[[Known problems and (Hopefully!) solutions]]

*:[[General information]]

*:[[Ideas]]

*:[[Gallery]]

*:[[scp via jump server]]

= Contacts =

:: Calem Hoffman mailto:crhoffman@anl.gov
:: Daniel Santiago-Gonzalez mailto:dasago@anl.gov
:: Sean A. Kuvin mailto:kuvin@anl.gov
:: Tsz Leung (Ryan) Tang mailto:ttang@anl.gov mailto:rtang@fsu.edu

{{Template:Standard Footer}}

Main Page

2024-01-09T20:54:54Z

Ttang: /* Hardware */

== HELIOS Digital DAQ Wiki Page ==

This is the wiki for all that is the [http://www.phy.anl.gov/atlas/helios HELIOS] Digital Data Acquisition (informally known as DigiOS).

For the kinematics of HELIOS, please look [[File:Kinematics of HELIOS.pdf|thumb]]

Online simulation is available [https://fsunuc.physics.fsu.edu/SOLARIS/ Here]

= Hardware =

{|class="wikitable"
!! Devices !! Function
|-
| Digitizers || digitizing analog signal
|-
| HELIOS DAQ || controlling and receiving data
|-
| Mac2020 || remote control of the HELIOS DAQ and online analysis
|-
| Mac2017 || Database, grafana, remote control of the WindowXP
|-
| WindowXP || HV control
|-
| HeliosDB (removed) || Database
|}

Here are more detail

*:[[Hardware]]

*:[[Locations]]

*:[[Hardware/Firmware Configurations]]

*:[[VME99 test stand IOC]]

*:[[Target Fan Control]]

*:[[Detectors]]

*:[[Alpha source]]

*:[[PV List]]

= Software =

*:[[GUI, Scripts And Analysis Code]]

*:[[Data Storage]]

*:[[Input/Output Control]]

*:[[EPIC]]

*:[[gtReceiver + GEBSort]]

*:[[Grafana + InfluxDB]]

*:[[Globus]]

*:[[Leakage Current from Iseg]]

*:[[Ptolemy in Mac using docker]]

= Usage and Operation =

*:[[System usage]]

*:[[Sorting Data]]

*:[["How to" for DAQ]]

*:[["How to" for analysis code]]

= Others =

*:[[Experiments]]

*:[[System testing]]

*:[[Known problems and (Hopefully!) solutions]]

*:[[General information]]

*:[[Ideas]]

*:[[Gallery]]

*:[[scp via jump server]]

= Contacts =

:: Calem Hoffman mailto:crhoffman@anl.gov
:: Daniel Santiago-Gonzalez mailto:dasago@anl.gov
:: Sean A. Kuvin mailto:kuvin@anl.gov
:: Tsz Leung (Ryan) Tang mailto:ttang@anl.gov mailto:rtang@fsu.edu

{{Template:Standard Footer}}

Main Page

2024-01-09T20:53:36Z

Ttang: /* Hardware */

== HELIOS Digital DAQ Wiki Page ==

This is the wiki for all that is the [http://www.phy.anl.gov/atlas/helios HELIOS] Digital Data Acquisition (informally known as DigiOS).

For the kinematics of HELIOS, please look [[File:Kinematics of HELIOS.pdf|thumb]]

Online simulation is available [https://fsunuc.physics.fsu.edu/SOLARIS/ Here]

= Hardware =

{|class="wikitable"
!! Devices !! Function
|-
| Digitizers || digitizing analog signal
|-
| HELIOS DAQ || controlling and receiving data
|-
| Mac2020 || remote control of the HELIOS DAQ and online analysis
|-
| Old Mac || Database, grafana, remote control of the WindowXP
|-
| WindowXP || HV control
|}

Here are more detail

*:[[Hardware]]

*:[[Locations]]

*:[[Hardware/Firmware Configurations]]

*:[[VME99 test stand IOC]]

*:[[Target Fan Control]]

*:[[Detectors]]

*:[[Alpha source]]

*:[[PV List]]

= Software =

*:[[GUI, Scripts And Analysis Code]]

*:[[Data Storage]]

*:[[Input/Output Control]]

*:[[EPIC]]

*:[[gtReceiver + GEBSort]]

*:[[Grafana + InfluxDB]]

*:[[Globus]]

*:[[Leakage Current from Iseg]]

*:[[Ptolemy in Mac using docker]]

= Usage and Operation =

*:[[System usage]]

*:[[Sorting Data]]

*:[["How to" for DAQ]]

*:[["How to" for analysis code]]

= Others =

*:[[Experiments]]

*:[[System testing]]

*:[[Known problems and (Hopefully!) solutions]]

*:[[General information]]

*:[[Ideas]]

*:[[Gallery]]

*:[[scp via jump server]]

= Contacts =

:: Calem Hoffman mailto:crhoffman@anl.gov
:: Daniel Santiago-Gonzalez mailto:dasago@anl.gov
:: Sean A. Kuvin mailto:kuvin@anl.gov
:: Tsz Leung (Ryan) Tang mailto:ttang@anl.gov mailto:rtang@fsu.edu

{{Template:Standard Footer}}

Scp via jump server

2023-12-24T18:40:09Z

Ttang: Created page with "The situation is, I want to download some files from digios1 (inside onenet) to my home, which is outside of the ANL network. digios1 --> jump server --> Home In Mac: scp -oProxyCommand="ssh -W %h:%p <USERNAME>@login.phy.anl.gov" helios@digios1:/PATH/TO/FILES HOME/PATH When scp support -J option scp -J <USERNAME>@login.phy.anl.gov helios@digios1:/PATH/TO/FILES HOME/PATH"

The situation is, I want to download some files from digios1 (inside onenet) to my home, which is outside of the ANL network.

digios1 --> jump server --> Home

In Mac:

scp -oProxyCommand="ssh -W %h:%p <USERNAME>@login.phy.anl.gov" helios@digios1:/PATH/TO/FILES HOME/PATH

When scp support -J option

scp -J <USERNAME>@login.phy.anl.gov helios@digios1:/PATH/TO/FILES HOME/PATH

Main Page

2023-12-24T18:36:48Z

Ttang: /* Others */

== HELIOS Digital DAQ Wiki Page ==

This is the wiki for all that is the [http://www.phy.anl.gov/atlas/helios HELIOS] Digital Data Acquisition (informally known as DigiOS).

For the kinematics of HELIOS, please look [[File:Kinematics of HELIOS.pdf|thumb]]

Online simulation is available [https://fsunuc.physics.fsu.edu/SOLARIS/ Here]

= Hardware =

*:[[Hardware]]

*:[[Locations]]

*:[[Hardware/Firmware Configurations]]

*:[[VME99 test stand IOC]]

*:[[Target Fan Control]]

*:[[Detectors]]

*:[[Alpha source]]

*:[[PV List]]

= Software =

*:[[GUI, Scripts And Analysis Code]]

*:[[Data Storage]]

*:[[Input/Output Control]]

*:[[EPIC]]

*:[[gtReceiver + GEBSort]]

*:[[Grafana + InfluxDB]]

*:[[Globus]]

*:[[Leakage Current from Iseg]]

*:[[Ptolemy in Mac using docker]]

= Usage and Operation =

*:[[System usage]]

*:[[Sorting Data]]

*:[["How to" for DAQ]]

*:[["How to" for analysis code]]

= Others =

*:[[Experiments]]

*:[[System testing]]

*:[[Known problems and (Hopefully!) solutions]]

*:[[General information]]

*:[[Ideas]]

*:[[Gallery]]

*:[[scp via jump server]]

= Contacts =

:: Calem Hoffman mailto:crhoffman@anl.gov
:: Daniel Santiago-Gonzalez mailto:dasago@anl.gov
:: Sean A. Kuvin mailto:kuvin@anl.gov
:: Tsz Leung (Ryan) Tang mailto:ttang@anl.gov mailto:rtang@fsu.edu

{{Template:Standard Footer}}

Main Page

2023-03-02T18:42:10Z

Ttang:

== HELIOS Digital DAQ Wiki Page ==

This is the wiki for all that is the [http://www.phy.anl.gov/atlas/helios HELIOS] Digital Data Acquisition (informally known as DigiOS).

For the kinematics of HELIOS, please look [[File:Kinematics of HELIOS.pdf|thumb]]

Online simulation is available [https://fsunuc.physics.fsu.edu/SOLARIS/ Here]

= Hardware =

*:[[Hardware]]

*:[[Locations]]

*:[[Hardware/Firmware Configurations]]

*:[[VME99 test stand IOC]]

*:[[Target Fan Control]]

*:[[Detectors]]

*:[[Alpha source]]

*:[[PV List]]

= Software =

*:[[GUI, Scripts And Analysis Code]]

*:[[Data Storage]]

*:[[Input/Output Control]]

*:[[EPIC]]

*:[[gtReceiver + GEBSort]]

*:[[Grafana + InfluxDB]]

*:[[Globus]]

*:[[Leakage Current from Iseg]]

*:[[Ptolemy in Mac using docker]]

= Usage and Operation =

*:[[System usage]]

*:[[Sorting Data]]

*:[["How to" for DAQ]]

*:[["How to" for analysis code]]

= Others =

*:[[Experiments]]

*:[[System testing]]

*:[[Known problems and (Hopefully!) solutions]]

*:[[General information]]

*:[[Ideas]]

*:[[Gallery]]

= Contacts =

:: Calem Hoffman mailto:crhoffman@anl.gov
:: Daniel Santiago-Gonzalez mailto:dasago@anl.gov
:: Sean A. Kuvin mailto:kuvin@anl.gov
:: Tsz Leung (Ryan) Tang mailto:ttang@anl.gov mailto:rtang@fsu.edu

{{Template:Standard Footer}}

File:Kinematics of HELIOS.pdf

2022-12-17T22:12:49Z

Ttang: Ttang uploaded a new version of File:Kinematics of HELIOS.pdf

Kinematics of HELIOS

File:Kinematics of HELIOS.pdf

2022-12-13T19:17:51Z

Ttang: Ttang uploaded a new version of File:Kinematics of HELIOS.pdf

Kinematics of HELIOS

Locations

2022-11-13T23:13:20Z

Ttang: /* DAQ Computer */

= Physical Location =

[[File:PhysicalLocation.png|800px|frameless]]

= Network Location Information =

A drawing of the network is like this (2021-01-21).

The CISCO router is the only way to the onenet and internet.

The HP Switch is a main switch for all devices, like the DAQ PC and the MAC.

The HELIOS-DB and the windowsXP connects to the onenet directly.


[[File:NetworkConnection20210121.png|800px|frameless]]

We added 2 Network Power switch

IP: 192.168.1.106 for Target fan
IP: 192.168.1.115 for DAQ

= DAQ Computer =
The data acquisition computer for digital HELIOS sits behind a NAT box. The NAT box is located at
digios1.onenet (192.168.203.52)
or from the Mac
192.168.1.2

The HELIOS-DB, Mac2017 and the windowsXP connect to the onenet, the IPs are

HELIOS-DB : 192.168.203.23 (nickname: heliosdb)

windowsXP : 192.168.203.37

mac2017 : 192.168.203.34 (nickname: mac2017)

= Login outside ANL =

only for PC at onenet.

ssh -J <username>@login.phy.anl.gov <accountName>@<onenet_IP>

{| class="wikitable"
|-
! PC
! accountName
! onenetIP
|-
| DAQ
| helios
| digios1
|-
| Mac2017
| heliosdigios
| mac2017
|}

= Nat Box / Rounter =
The login for the cisco ([http://www.cisco.com/c/en/us/products/collateral/routers/rv180-vpn-router/c78-697397_data_sheet.html cisco data page]) is uname ''cisco'' and the gammasphere password
192.168.1.1
Notes on cisco setup:
network -> wan -> iPv4 -> static -> 192.168.203.52 -> default .1 -> DNS .1

IOC's are
192.168.1.2X
DAQ computer (digios1) is
192.168.1.2
MAC2020 computer (helios-iMac) is
192.168.1.164
Target Fan power switch (target-pwrswitch) is
192.168.1.106
DAQ power switch is
192.168.1.115

There are some unknown IP
192.168.1.3
192.168.1.81

To scan all "active" devices in the CISCO network:
$nmap -F 192.168.1.*

= Terminal Server =
[https://www.digi.com/pdf/prd_ts_portserverts816.pdf Portserver TS16 MEI]

Info? (2.6.23-431.5.1.el6.i686 (RH 4.4.7-3)
Login with ''root'' and gammasphere pswrd

telnet 192.168.1.3 200[1-X]

In the DAQ-PC, the IP and the corresponding "nickname" are saved in
/etc/hosts

$cat /etc/hosts
127.0.0.1 localhost.localdomain localhost
::1 localhost6.localdomain6 localhost6
192.168.1.1 digios1
192.168.1.3 ts
192.168.1.20 ioc0
192.168.1.21 ioc1
192.168.1.22 ioc2
192.168.1.23 ioc3
192.168.1.24 ioc4
192.168.1.234 tllptgs

== Physical Locations and ID's of Digitizers / Routers / Triggers ==

Really need a few figures with labels / diagrams.

* Serial numbers of system hardware
* Board ID numbers for data processing
* IP address and names of modules

"How to" for analysis code

2022-04-29T19:29:35Z

Ttang:

[last updated Mar 28, 2022]

Everything should be performed in '''digios/analysis/working''' directory,

{| class="wikitable"
|-
|ATTENTION:
|-
|txt file extension is editable for user.
|-
|dat files extension is not supposed to be edited, they are generated.
|-
|Editable file name will be highlighted with blue color
|}

= Overview =

[[File:Screenshot 2022-03-28 023801.png|1200px|frameless]]

= General Usage =

== How to download the source code ? ==

make sure you have git in your computer.

in the directory you like to put in the code. for example, I like to put the code in ~/, then >cd ~/

~/>git clone https://github.com/calemhoffman/digios.git

you will see a folder name digios is there.

digios>cd digios

digios>git status

To check your experiment

digios>git branch -a

for example your experiment is using the branch h064_15N

digios>git status

you will see you are in the branch for your experiment.

for analysis, you only need the things inside digios/analysis

Make sure you create folders or symbolic links for data, merged_data, and root_data under digios/analysis.

== How to update source code ? ==

The easiest easy is to restore everything that changed.

digios>git reset --hard

after resetting the folder, we can update the code by

digios>git pull

== How to get option for a method or function ? ==

For most of the bash script, if you have no argument or the argument is "-help" it will display help message

working>Process_run

working>../Cleopatra/Transfer -help

For most root macro, for example, RDTCutsCreator(),
after typed the first bracket, use tab, it will display the arguments.

root>RDTCutsCreator(

then press tab. it will show

root>RDTCutsCreator(TString filename, TString saveFileName = "rdtCuts.root", int eRange = 4000, int eRange = 60000 )

== How to take a screenshot in MAC ? ==

Command + Shift + 4 = screenshot selected area

Command + Shift + 4, then space_bar = screenshot selected window

== How to check the start time and stop time for a run? ==

in digios/analysis/data, there is RunTimeStamp.dat.
this file stored all start and stop time for all runs.

in MAC or DAQ,

anywhere>ShowRunTimeStamp

== How to check the raw files for a run? ==

in MAC or DAQ

anywhere>ShowRunSize [RUNNUM]

= Git Branch Management =

== How to Setup/Switch for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Has to be done in the DAQ first
|-
|CAUTION: Has to be done in the MAC after
|}

given that the digios directory is clean, meaning

digios>git status

show no file is modified.

If you are not in the master branch

digios>./SetUpNewExp master

Then you are ready to setup a new experimental branch by

digios>./SetUpNewExp [new experiment name]

The bash script with do all the work.

After that, do the same in the MAC.

----------

When the folder is not clean. i.e., not everything git committed. The SetUpNewExp will stop and not switch branches or make a new experiment.

In that case, the simplest way is

digios>git add -A # add all changes to stage
digios>git commit -m "comment you like" # commit the change and make the folder clean

Or, you want to discard all change

digios>git reset --hard

== How to clean up the working directory and prepare for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Need to be done in both MAC and DAQ
|-
|CAUTION: !!! READ till the end before you do anything!!!!
|}

After each experiment, the files in digios directory would be changed.

To check the change,

DAQ>cd ~/digios

digios>git status

To snapshot the change

digios>git add -A
digios>git commit -m "comment for this snapshot"

It is better to push the snapshot to the github

digios>git push origin [branch name]

{| class="wikitable"
|-
|CAUTION: Also need to git the DAQ!
|-
|CAUTION: The files in the DAQ and the MAC could be both changed. Mostly, the change in the DAQ is in digios/daq.
|-
|CAUTION: That means the DAQ and MAC has to be merged.
|}

<s>We use a merge driver that the expName.sh will not be merged. The detail can be found in .gitattribute and git documentation. </s>

It is better to start with the DAQ.
# commit and push the daq/edm/scripts folder
# commit and push the daq/edm/screens (if anything changed)

and then, go to the Mac,
# fetch and merge, since the DAQ pushed latest commit
# commit and push the analysis/Armory/
# commit and push the analysis/Cleopatra
# commit and push the analysis/working

Now, we can go to LCRC ( /lcrc/project/HELIOS/digios )
The LCRC always in master branch.
then we can merge and solve conflict for each commit from the experiment.

After above action, we can go back to the DAQ, and commit the expName.sh, and switch back to master branch or setup a new experiment.

= Process Run online =

== How to process run? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/GEBSort, and
GEBSort>make offline
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

working>Process_RUN [RUNNUM]

The bash script will download run [RUNNUM], merge, event building, GeneralSort (mapping), and Monitors.C

to see more options, ./process_run without any argument

working>Process_RUN
Process_RUN [RunNum] [Merge] [EventBuild] [GeneralSort] [Monitor]"
RunNum = run number / \"lastRun\" "
Merge = 1/0/-1 || 1 = merge, 0 = not merge, -1 = force merge "
EventBld = 2/1/0/-1/-2 || 2 = with Trace"
GenralSort = n/1/0/-1/-n || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker"
Monitors = 2/1/0 || 1 = single run, 2 = using the list in ChainMonitors.C"
10 = single run and post to websrv, 20 = list runs and post to websrv"

**** When feeding trace data to Monitors, the EventBld flag must be 2 or -2."

The working flow of process_run (without Monitor) is

[[File:Process run.png|600px|frameless]]

For data calibration, see [[GUI,_Scripts_And_Analysis_Code#Standard_data_analysis_flow|standard data analysis flow]]

== How to process multiple runs at once ? ==
{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

$./process_MultiRuns [RunNum1] [RunNum2] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to process multiple runs as a slurm job? ==

{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

A slurm job is a job in LCRC. The script will generate the slurm.sh and submit the job to 1 node.

If only merge and build event, only 1 core will be used.
If with GeneralSort, 36 cores will be used.

$./process_Slurm [RunNum1] [RunNum2] [time] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
time = allocate time
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to manually run the Monitors.C for a given run? ==

make sure gen_runXXX.root is generated in digios/analysis/root_data.

working>root ../root_data/gen_runXXX.root

working>gen_tree->Process("Monitors.C+")

== How to "Monitor" multiple runs ? ==

edit ChainMonitors.C 

you can see it use the TChain class.

to add files, for example, add the run 33 to 40, 42, 45, and 50, and I assume the run 33 to 40, 42, and 45 are already downloaded

chain->Add("../root_data/gen_run03[3-9].root");
chain->Add("../root_data/gen_run04[0,2,5].root");
chain->Add("../root_data/gen_run050.root");

Then, in process_run

working>./process_run 50 1 1 1 2

Notice that it will download, merge, build event, and GeneralSort (mapping) for run 50 ONLY.

= How to change the array position ? =

edit the file detectorGeo.txt

== How to Donwload all runs into the Mac ? ==

working>Rsyn_data_from_DAQ.sh

== How to change or add a recoil Cuts ? ==

see [[#How to use RDTCutsCreator ?]]

== How to use RDTCutsCreator ? ==

After ./process_run, the ../Armory/RDTCutsCreator.C will be loaded.

root>RDTCutsCreator( [filename], [save file name], [E range], [dE range] )

The default [save file name] is "rdtCuts.root". If you like to use other [save file name], please correct the TString rdtCutFile in Monitors.C

if something go wrong during the RDTCutsCreator, simply delete the "rdtCuts.root".

There is a way to include multiple files for the RDTCutsCreator

root>RDTCutsCreator("../root_data/gen_run02[3-7].root")

or

root>RDTCutsCreator("../root_data/gen_run02[3,5,7,9].root")

To include more files, we can edit ../Armory/RDTCutsCreator.C

inside the file, manual add the files. To run that script.

working> root

root>.L ../Armory/RDTCutsCreator.C

root>RDTCutCreator("", [save file name], [E range], [dE range] )

= How is the Calibration flow ? =
[[File:DataAnalysis.png|800px|frameless]]

The calibration has few steps:
# Gain-matching with xn to xf
# Gain-matching with xn'+xf to e
# Calibrate e

To do step 1, It is better start with alpha data, because the alpha data is independent of position. By gating on 1 of the alpha peak, then plot the xf vs xn, the gain matching of xn to xf can be easily done. And because we need to gate on the alpha peak, then why not do a calibration on the energy using alpha data? So, in the Cali_xf_xn.C, the program will first calibrate alpha energy, then gate on 1 of the alpha peak to do gain match xn to xf.

To do step 2, we need a gain-matched xn, i.e. xn', so that xn'+xf should be proportional to the raw e.

In order to calibrate the energy, sometimes, alpha calibration is doing a good job, given that the alpha source is a good source. However, we can also calibrate the energy using kinematic E-Z lines. See [["How_to"_for_analysis_code#How to Calibrate reaction data by kinematics ?| How to Calibrate reaction data by kinematics ?]]

== How to Calibrate alpha data ? ==

If statistics for single detector is sufficient, i.e. all peak is clearly identified.

edit the file ChainMonitors.C

working>root AutoCalibrationTrace.C+

select option 0

It will guide you through the process.

-----------------------------

If statistics is not so good, we can use the ../Armory/Cali_e_single.C

== How to Gain matching of xn to xf ? ==

working>root AutoCalibrationTrace.C+

select option 0

First, it will go through energy calibration, it does not need to be good.

Next, select any peak, so that the program will gate on that peak and plot xf vs xn. From there, the xn will gain match xf.

== How to gain match the xn+xf to raw e ? ==

To properly do so, you have to gain-matched xn to xf. Then

working>root AutoCalibrationTrace.C+

select option 1

This has to be NOT alpha run, just any beam run. It will plot the raw e vs xf + xn'.

== How to Calibrate reaction data by kinematics ? ==

( I know It needs more detail )

ONLY for sufficient statistic for individual detector.

edit the file ChainMonitors.C

working>root AutoCalibrationtrace.C+

select option 2

it will guide you through.

---------------
In order to speed up the process, it will create a temp.root. a root file only contain e and z.

User can use ../Armory/Check_e_x.root and create a cut to be used in the Monte-Carlo process.

== How to output a root file only contain physical data ? ==

after the calibration is done, we can edit ChainMonitors.C

and run

working>root AutoCalibrationTrace.C+

Select option 3 to generate the A_gen_runXXX.root

[[File:Option3.png|600px|frameless]]

= Kinematic and DWBA Calculation =

The simplest way is using the Simulation_Helper.C. This is a GUI interface.

working>root Simulation_Helper.C

[[File:Simulation Helper screenshot.png|800px|frameless|none]]

== How to change the calculation for Ex and thetaCM ? ==

edit the file reactionConfig.txt, than recalculate the reaction.dat by running ../Cleopatra/Transfer

working>../Cleopatra/Transfer

== How to change the kinematic E-Z line? ==

see [[#How to simulate the kinematics?]]

The E-Z lines are stored in fxList in transfer.root

In Monitors.C, at the end or Monitors::Terminate().

you can see the fxList.

== How to simulate the kinematics? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|}

edit
* reactionConfig.txt 
* detectorGeo.txt 
* Ex.txt 

Then run
working>../Cleopatra/Transfer

after that, 2 files will be generated, 1) reaction.dat, 2) transfer.root

a tree is inside transfer.root.

you can see the tree branches by

root> tree->Print()

I hope the branch name is self-explained.

In Armory, there is a root macro Check_Transfer.C

working>root '../Armory/Check_Transfer.C("transfer.root")'

The macro load the transfer.root and plot the e-z plot, the recoil, recoil radius vs thetaCM etc...

== How to do DWBA calculation ? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|-
|CAUTION: ONLY IN LINUX, because Ptolemy only work in Linux.
|}

edit the file DWBA, then

working>./Cleopatra example 1 1 1 1 0 [minAng] [maxAng] [angStep]

This will generate the example.in, feed to Ptolemy, output example.out, extract the differential cross section into

* example.Xsec.txt
* example.root

And plot the d.s.c. using example.root

It will also generate example.Ex.txt

For arguments meaning, use Cleopatra without any argument

working>./Cleopatra

== How to do kinematics simulation with DWBA differential cross section ? ==

see [[#How to do DWBA calculation ?]] first.

edit
* reactionConfig.txt 
* detectorGeo.txt 
* example 

Make sure the reaction in the reactionConfig.txt is matching with that in example

working>./Cleopatra example 1 1 1 0 1 0 180 1

The excitation levels is using example.Ex.txt.

The bash script will calculate the DWBA d.s.c. using Cleopatra, then using ../Cleopatra/Transfer to do the simulation.

see [[#How to simulate the kinematics?]]

= How to do trace analysis ? =

updated Feb-12, 2021

simply

working>Process_RUN [RunNum] 1 -2 [number_of_worker] [Option_for_Monitors]

Updated Nov-6, 2019
The GEBSort_nogeb_trace was generated, Simple run ./process_run with option is fine

--------------------------------
First, the GEBSort code has to be recompile by changing the file digios/GEBSort/bin_rcnp.C

in that file, comment out the trace (line ?)

Then, recompile

GEBSort>make offline

Now the gen_runXXX.root will contains trace data.

go back to working directory

working>./process_run [RUNNUM] 1 1 2 1

The 4th argument is 2, that means the GeneralSort (or the mapping ) will use ../Amrory/GeneralSortTrace.C instead of ../Amory/GeneralSort.C

The 4th argument can be also be more than 2, say, when it is N, it means it will use Proof, a parallel computing framework built-in in root that use N cores.

To display the trace, we can use ../Armory/readTrace.C ( this macro is kind of shitty.....)

= How to count a 1D histogram for a given range ? =

After ./process_run, a function Check1D() is loaded.

= How to fit the excitation spectrum ? =

If the reaction.dat is set properly, after ./process_run, the excite() function will give you the excitation spectrum.

root>excite()

You can use the fitAuto() function to auto fit the spectrum by

root>fitAuto(hEx)

For more option

fitAuto( [hist name], [BG estimation] )

-------------------------------
Or you can can fit N-Gauss + 1 linear function. In this case, edit the AutFit_para.txt

root>fitNGaussP1(hEx)

Detectors

2022-04-20T17:39:58Z

Ttang: /* CSD */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= CSD =

(crazy spider detector)

[[File:CSD PBC mount.jpg|frameless|none]]

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

{| class="wikitable"
|+ Dimension
|-
| area || 400 mm2
|-
| Thickness || can-stop-carbon-thick
|}

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

{| class="wikitable"
|+ dimension
|-
| Blocker ||inner 15 mm, outer 60 mm
|-
| Detector || inner 24 mm, outer 48 mm
|-
| thickness || can-stop-carbon-thick ~ 10 MeV/u
|}

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

File:CSD PBC mount.jpg

2022-04-20T17:39:45Z

Ttang:

PBC mount for the CSD

Detectors

2022-03-31T22:22:37Z

Ttang:

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= CSD =

(crazy spider detector)

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

{| class="wikitable"
|+ Dimension
|-
| area || 400 mm2
|-
| Thickness || can-stop-carbon-thick
|}

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

{| class="wikitable"
|+ dimension
|-
| Blocker ||inner 15 mm, outer 60 mm
|-
| Detector || inner 24 mm, outer 48 mm
|-
| thickness || can-stop-carbon-thick ~ 10 MeV/u
|}

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:19:16Z

Ttang: /* Elum 2 or S1 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

{| class="wikitable"
|+ Dimension
|-
| area || 400 mm2
|-
| Thickness || can-stop-carbon-thick
|}

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

{| class="wikitable"
|+ dimension
|-
| Blocker ||inner 15 mm, outer 60 mm
|-
| Detector || inner 24 mm, outer 48 mm
|-
| thickness || can-stop-carbon-thick ~ 10 MeV/u
|}

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:18:08Z

Ttang: /* Elum 1 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

{| class="wikitable"
|+ Dimension
|-
| area || 400 mm2
|-
| Thickness || can-stop-carbon-thick
|}

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

thickness : can-stop-carbon-thick

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:17:06Z

Ttang: /* Elum 2 or S1 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension: 400 mm^2
Thickness: can-stop-carbon-thick

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

thickness : can-stop-carbon-thick

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:16:44Z

Ttang: /* Elum 1 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension: 400 mm^2
Thickness: can-stop-carbon-thick

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:16:18Z

Ttang: /* Elum 1 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension: 400 mm^2
Thickness: ?

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:10:10Z

Ttang: /* Position sensitive Si-detector arrays */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first) (thickness?)
[[File:OldArray.png|700px|frameless]]

* 6 side x 5 (2019-March) (no longer exist)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension??

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:09:08Z

Ttang: /* Elum 2 or S1 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension??

== Elum 2 or S1 ==
[[File:Elum2.jpg|500px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:08:43Z

Ttang: /* Recoil detectors */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|-
| || || Sharpy
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension??

== Elum 2 or S1 ==
[[File:Elum2.jpg|800px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T22:07:50Z

Ttang: /* Recoil detectors */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|}

[[File:Recoil detector and connection.png|500px|frameless]]

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension??

== Elum 2 or S1 ==
[[File:Elum2.jpg|800px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

File:Recoil detector and connection.png

2022-03-31T22:07:41Z

Ttang:

recoil detector and connection

Detectors

2022-03-31T22:03:13Z

Ttang: /* Recoil detectors */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

[[File:Recoil detectors.jpg|600px|frameless]]

There are QQQ1 detector from micron

http://www.micronsemiconductor.co.uk/product/qqq1/

{| class="wikitable"
|+ List of Recoil detector
|-
! Number !! Thickness [um] !! Belong to
|-
| 2259-29? || 989 || Alan
|-
| 1419-22? || 1475 || Alan
|-
| 2259-25? || 984 || Alan
|-
| 2259-39? || 995 || Alan
|}

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension??

== Elum 2 or S1 ==
[[File:Elum2.jpg|800px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

File:Recoil detectors.jpg

2022-03-31T22:00:16Z

Ttang:

image of recoil detectors

Detectors

2022-03-31T21:53:11Z

Ttang: /* S1 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== Elum 1 ==

[[File:Elum1.jpg|600px|frameless]]

Dimension??

== Elum 2 or S1 ==
[[File:Elum2.jpg|800px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

File:Elum1.jpg

2022-03-31T21:52:56Z

Ttang:

Elum 1

Detectors

2022-03-31T21:49:49Z

Ttang: /* Elum 2 */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== S1 ==

== Elum 2 or S1 ==
[[File:Elum2.jpg|800px|frameless]]

[[File:S1.jpg|500px|frameless]]

http://www.micronsemiconductor.co.uk/product/s1/

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 24 mm, outer 48 mm

numbers of channel 16.

Connection to preamp. only 1 side is connected. another side is biased.

(picture of connection )

Detectors

2022-03-31T21:47:22Z

Ttang: /* Elum detectors */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

== S1 ==

== Elum 2 ==
[[File:Elum2.jpg|800px|frameless]]

[[File:S1.jpg|500px|frameless]]

number of channel 16.

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 20 mm, outer 50 mm

File:S1.jpg

2022-03-31T21:47:13Z

Ttang:

The picture is copy from http://www.micronsemiconductor.co.uk/product/s1/

Detectors

2022-03-31T21:44:38Z

Ttang: /* Elum detectors */

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

[[File:Elum2.jpg|800px|frameless]]

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 20 mm, outer 50 mm

Detectors

2022-03-31T21:43:25Z

Ttang:

= Position sensitive Si-detector arrays =

We have 2 arrays
* 4 side x 6 (first)
[[File:OldArray.png|500px|frameless]]
* 6 side x 5 (2019-March)
[[File:NewArray.png|800px|frameless]]

= Recoil detectors =

== detector holder ==

= Elum detectors =

We have 2 Elum detectors.

[[File:Elum2.jpg|1000px|frameless]]

The dimension is
* Blocker : inner 15 mm, outer 60 mm
* Detector : inner 20 mm, outer 50 mm

File:Elum2.jpg

2022-03-31T21:42:21Z

Ttang:

elum2

Ptolemy in Mac using docker

2022-03-31T21:11:56Z

Ttang: Created page with "== Installation instructions == === Install Docker Desktop for Mac. === https://download.docker.com/mac/stable/Docker.dmg Start the app. If it is running, the docker i..."

== Installation instructions ==

=== Install Docker Desktop for Mac. ===

https://download.docker.com/mac/stable/Docker.dmg

Start the app. If it is running, the docker icon (a whale stacked with container boxes) should be present on the top menu bar on the right hand side.

=== Open a terminal window and type the following at the command prompt : ===

$ docker pull tehatanlgov/ptolemy:latest

This downloads the ptolemy container from docker hub. You need do this only once. List downloaded containers with :

$ docker images

=== Make a bash script ===

#!/bin/bash
docker run --rm -i -w $PWD tehatanlgov/ptolemy

In digios repository, there is already digios/analysis/Cleopatra/ptolemy_mac, which is executable.

=== Run Ptolemy ===

Cleopatra$ptolemy_mac <infile> <outfile>

Main Page

2022-03-31T17:54:01Z

Ttang: /* Software */

== HELIOS Digital DAQ Wiki Page ==

This is the wiki for all that is the [http://www.phy.anl.gov/atlas/helios HELIOS] Digital Data Acquisition (informally known as DigiOS).

For the kinematics of HELIOS, please look [[File:Kinematics of HELIOS.pdf|thumb]]

= Hardware =

*:[[Hardware]]

*:[[Locations]]

*:[[Hardware/Firmware Configurations]]

*:[[VME99 test stand IOC]]

*:[[Target Fan Control]]

*:[[Detectors]]

*:[[Alpha source]]

*:[[PV List]]

= Software =

*:[[GUI, Scripts And Analysis Code]]

*:[[Data Storage]]

*:[[Input/Output Control]]

*:[[EPIC]]

*:[[gtReceiver + GEBSort]]

*:[[Grafana + InfluxDB]]

*:[[Globus]]

*:[[Leakage Current from Iseg]]

*:[[Ptolemy in Mac using docker]]

= Usage and Operation =

*:[[System usage]]

*:[[Sorting Data]]

*:[["How to" for DAQ]]

*:[["How to" for analysis code]]

= Others =

*:[[Experiments]]

*:[[System testing]]

*:[[Known problems and (Hopefully!) solutions]]

*:[[General information]]

*:[[Ideas]]

*:[[Gallery]]

= Contacts =

:: Calem Hoffman mailto:crhoffman@anl.gov
:: Daniel Santiago-Gonzalez mailto:dasago@anl.gov
:: Sean A. Kuvin mailto:kuvin@anl.gov
:: Tsz Leung (Ryan) Tang mailto:ttang@anl.gov mailto:rtang@fsu.edu

{{Template:Standard Footer}}

"How to" for analysis code

2022-03-28T06:49:53Z

Ttang: /* General Usage */

[last updated Mar 28, 2022]

Everything should be performed in digios/analysis/working directory,

{| class="wikitable"
|-
|ATTENTION:
|-
|txt file extension is editable for user.
|-
|dat files extension is not supposed to be edited, they are generated.
|-
|Editable file name will be highlighted with blue color
|}

= Overview =

[[File:Screenshot 2022-03-28 023801.png|1200px|frameless]]

= General Usage =

== How to download the source code ? ==

make sure you have git in your computer.

in the directory you like to put in the code. for example, I like to put the code in ~/, then >cd ~/

~/>git clone https://github.com/calemhoffman/digios.git

you will see a folder name digios is there.

digios>cd digios

digios>git status

To check your experiment

digios>git branch -a

for example your experiment is using the branch h064_15N

digios>git status

you will see you are in the branch for your experiment.

for analysis, you only need the things inside digios/analysis

Make sure you create folders or symbolic links for data, merged_data, and root_data under digios/analysis.

== How to update source code ? ==

The easiest easy is to restore everything that changed.

digios>git reset --hard

after resetting the folder, we can update the code by

digios>git pull

== How to get option for a method or function ? ==

For most of the bash script, if you have no argument or the argument is "-help" it will display help message

working>Process_run

working>../Cleopatra/Transfer -help

For most root macro, for example, RDTCutsCreator(),
after typed the first bracket, use tab, it will display the arguments.

root>RDTCutsCreator(

then press tab. it will show

root>RDTCutsCreator(TString filename, TString saveFileName = "rdtCuts.root", int eRange = 4000, int eRange = 60000 )

== How to take a screenshot in MAC ? ==

Command + Shift + 4 = screenshot selected area

Command + Shift + 4, then space_bar = screenshot selected window

== How to check the start time and stop time for a run? ==

in digios/analysis/data, there is RunTimeStamp.dat.
this file stored all start and stop time for all runs.

in MAC or DAQ,

anywhere>ShowRunTimeStamp

== How to check the raw files for a run? ==

in MAC or DAQ

anywhere>ShowRunSize [RUNNUM]

= Git Branch Management =

== How to Setup/Switch for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Has to be done in the DAQ first
|-
|CAUTION: Has to be done in the MAC after
|}

given that the digios directory is clean, meaning

digios>git status

show no file is modified.

If you are not in the master branch

digios>./SetUpNewExp master

Then you are ready to setup a new experimental branch by

digios>./SetUpNewExp [new experiment name]

The bash script with do all the work.

After that, do the same in the MAC.

----------

When the folder is not clean. i.e., not everything git committed. The SetUpNewExp will stop and not switch branches or make a new experiment.

In that case, the simplest way is

digios>git add -A # add all changes to stage
digios>git commit -m "comment you like" # commit the change and make the folder clean

Or, you want to discard all change

digios>git reset --hard

== How to clean up the working directory and prepare for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Need to be done in both MAC and DAQ
|-
|CAUTION: !!! READ till the end before you do anything!!!!
|}

After each experiment, the files in digios directory would be changed.

To check the change,

DAQ>cd ~/digios

digios>git status

To snapshot the change

digios>git add -A
digios>git commit -m "comment for this snapshot"

It is better to push the snapshot to the github

digios>git push origin [branch name]

{| class="wikitable"
|-
|CAUTION: Also need to git the DAQ!
|-
|CAUTION: The files in the DAQ and the MAC could be both changed. Mostly, the change in the DAQ is in digios/daq.
|-
|CAUTION: That means the DAQ and MAC has to be merged.
|}

<s>We use a merge driver that the expName.sh will not be merged. The detail can be found in .gitattribute and git documentation. </s>

It is better to start with the DAQ.
# commit and push the daq/edm/scripts folder
# commit and push the daq/edm/screens (if anything changed)

and then, go to the Mac,
# fetch and merge, since the DAQ pushed latest commit
# commit and push the analysis/Armory/
# commit and push the analysis/Cleopatra
# commit and push the analysis/working

Now, we can go to LCRC ( /lcrc/project/HELIOS/digios )
The LCRC always in master branch.
then we can merge and solve conflict for each commit from the experiment.

After above action, we can go back to the DAQ, and commit the expName.sh, and switch back to master branch or setup a new experiment.

= Process Run online =

== How to process run? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/GEBSort, and
GEBSort>make offline
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

working>Process_RUN [RUNNUM]

The bash script will download run [RUNNUM], merge, event building, GeneralSort (mapping), and Monitors.C

to see more options, ./process_run without any argument

working>Process_RUN
Process_RUN [RunNum] [Merge] [EventBuild] [GeneralSort] [Monitor]"
RunNum = run number / \"lastRun\" "
Merge = 1/0/-1 || 1 = merge, 0 = not merge, -1 = force merge "
EventBld = 2/1/0/-1/-2 || 2 = with Trace"
GenralSort = n/1/0/-1/-n || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker"
Monitors = 2/1/0 || 1 = single run, 2 = using the list in ChainMonitors.C"
10 = single run and post to websrv, 20 = list runs and post to websrv"

**** When feeding trace data to Monitors, the EventBld flag must be 2 or -2."

The working flow of process_run (without Monitor) is

[[File:Process run.png|600px|frameless]]

For data calibration, see [[GUI,_Scripts_And_Analysis_Code#Standard_data_analysis_flow|standard data analysis flow]]

== How to process multiple runs at once ? ==
{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

$./process_MultiRuns [RunNum1] [RunNum2] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to process multiple runs as a slurm job? ==

{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

A slurm job is a job in LCRC. The script will generate the slurm.sh and submit the job to 1 node.

If only merge and build event, only 1 core will be used.
If with GeneralSort, 36 cores will be used.

$./process_Slurm [RunNum1] [RunNum2] [time] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
time = allocate time
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to manually run the Monitors.C for a given run? ==

make sure gen_runXXX.root is generated in digios/analysis/root_data.

working>root ../root_data/gen_runXXX.root

working>gen_tree->Process("Monitors.C+")

== How to "Monitor" multiple runs ? ==

edit ChainMonitors.C 

you can see it use the TChain class.

to add files, for example, add the run 33 to 40, 42, 45, and 50, and I assume the run 33 to 40, 42, and 45 are already downloaded

chain->Add("../root_data/gen_run03[3-9].root");
chain->Add("../root_data/gen_run04[0,2,5].root");
chain->Add("../root_data/gen_run050.root");

Then, in process_run

working>./process_run 50 1 1 1 2

Notice that it will download, merge, build event, and GeneralSort (mapping) for run 50 ONLY.

= How to change the array position ? =

edit the file detectorGeo.txt

== How to Donwload all runs into the Mac ? ==

working>Rsyn_data_from_DAQ.sh

== How to change or add a recoil Cuts ? ==

see [[#How to use RDTCutsCreator ?]]

== How to use RDTCutsCreator ? ==

After ./process_run, the ../Armory/RDTCutsCreator.C will be loaded.

root>RDTCutsCreator( [filename], [save file name], [E range], [dE range] )

The default [save file name] is "rdtCuts.root". If you like to use other [save file name], please correct the TString rdtCutFile in Monitors.C

if something go wrong during the RDTCutsCreator, simply delete the "rdtCuts.root".

There is a way to include multiple files for the RDTCutsCreator

root>RDTCutsCreator("../root_data/gen_run02[3-7].root")

or

root>RDTCutsCreator("../root_data/gen_run02[3,5,7,9].root")

To include more files, we can edit ../Armory/RDTCutsCreator.C

inside the file, manual add the files. To run that script.

working> root

root>.L ../Armory/RDTCutsCreator.C

root>RDTCutCreator("", [save file name], [E range], [dE range] )

= How is the Calibration flow ? =
[[File:DataAnalysis.png|800px|frameless]]

The calibration has few steps:
# Gain-matching with xn to xf
# Gain-matching with xn'+xf to e
# Calibrate e

To do step 1, It is better start with alpha data, because the alpha data is independent of position. By gating on 1 of the alpha peak, then plot the xf vs xn, the gain matching of xn to xf can be easily done. And because we need to gate on the alpha peak, then why not do a calibration on the energy using alpha data? So, in the Cali_xf_xn.C, the program will first calibrate alpha energy, then gate on 1 of the alpha peak to do gain match xn to xf.

To do step 2, we need a gain-matched xn, i.e. xn', so that xn'+xf should be proportional to the raw e.

In order to calibrate the energy, sometimes, alpha calibration is doing a good job, given that the alpha source is a good source. However, we can also calibrate the energy using kinematic E-Z lines. See [["How_to"_for_analysis_code#How to Calibrate reaction data by kinematics ?| How to Calibrate reaction data by kinematics ?]]

== How to Calibrate alpha data ? ==

If statistics for single detector is sufficient, i.e. all peak is clearly identified.

edit the file ChainMonitors.C

working>root AutoCalibrationTrace.C+

select option 0

It will guide you through the process.

-----------------------------

If statistics is not so good, we can use the ../Armory/Cali_e_single.C

== How to Gain matching of xn to xf ? ==

working>root AutoCalibrationTrace.C+

select option 0

First, it will go through energy calibration, it does not need to be good.

Next, select any peak, so that the program will gate on that peak and plot xf vs xn. From there, the xn will gain match xf.

== How to gain match the xn+xf to raw e ? ==

To properly do so, you have to gain-matched xn to xf. Then

working>root AutoCalibrationTrace.C+

select option 1

This has to be NOT alpha run, just any beam run. It will plot the raw e vs xf + xn'.

== How to Calibrate reaction data by kinematics ? ==

( I know It needs more detail )

ONLY for sufficient statistic for individual detector.

edit the file ChainMonitors.C

working>root AutoCalibrationtrace.C+

select option 2

it will guide you through.

---------------
In order to speed up the process, it will create a temp.root. a root file only contain e and z.

User can use ../Armory/Check_e_x.root and create a cut to be used in the Monte-Carlo process.

== How to output a root file only contain physical data ? ==

after the calibration is done, we can edit ChainMonitors.C

and run

working>root AutoCalibrationTrace.C+

Select option 3 to generate the A_gen_runXXX.root

[[File:Option3.png|600px|frameless]]

= Kinematic and DWBA Calculation =

The simplest way is using the Simulation_Helper.C. This is a GUI interface.

working>root Simulation_Helper.C

[[File:Simulation Helper screenshot.png|800px|frameless|none]]

== How to change the calculation for Ex and thetaCM ? ==

edit the file reactionConfig.txt, than recalculate the reaction.dat by running ../Cleopatra/Transfer

working>../Cleopatra/Transfer

== How to change the kinematic E-Z line? ==

see [[#How to simulate the kinematics?]]

The E-Z lines are stored in fxList in transfer.root

In Monitors.C, at the end or Monitors::Terminate().

you can see the fxList.

== How to simulate the kinematics? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|}

edit
* reactionConfig.txt 
* detectorGeo.txt 
* Ex.txt 

Then run
working>../Cleopatra/Transfer

after that, 2 files will be generated, 1) reaction.dat, 2) transfer.root

a tree is inside transfer.root.

you can see the tree branches by

root> tree->Print()

I hope the branch name is self-explained.

In Armory, there is a root macro Check_Transfer.C

working>root '../Armory/Check_Transfer.C("transfer.root")'

The macro load the transfer.root and plot the e-z plot, the recoil, recoil radius vs thetaCM etc...

== How to do DWBA calculation ? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|-
|CAUTION: ONLY IN LINUX, because Ptolemy only work in Linux.
|}

edit the file DWBA, then

working>./Cleopatra example 1 1 1 1 0 [minAng] [maxAng] [angStep]

This will generate the example.in, feed to Ptolemy, output example.out, extract the differential cross section into

* example.Xsec.txt
* example.root

And plot the d.s.c. using example.root

It will also generate example.Ex.txt

For arguments meaning, use Cleopatra without any argument

working>./Cleopatra

== How to do kinematics simulation with DWBA differential cross section ? ==

see [[#How to do DWBA calculation ?]] first.

edit
* reactionConfig.txt 
* detectorGeo.txt 
* example 

Make sure the reaction in the reactionConfig.txt is matching with that in example

working>./Cleopatra example 1 1 1 0 1 0 180 1

The excitation levels is using example.Ex.txt.

The bash script will calculate the DWBA d.s.c. using Cleopatra, then using ../Cleopatra/Transfer to do the simulation.

see [[#How to simulate the kinematics?]]

= How to do trace analysis ? =

updated Feb-12, 2021

simply

working>Process_RUN [RunNum] 1 -2 [number_of_worker] [Option_for_Monitors]

Updated Nov-6, 2019
The GEBSort_nogeb_trace was generated, Simple run ./process_run with option is fine

--------------------------------
First, the GEBSort code has to be recompile by changing the file digios/GEBSort/bin_rcnp.C

in that file, comment out the trace (line ?)

Then, recompile

GEBSort>make offline

Now the gen_runXXX.root will contains trace data.

go back to working directory

working>./process_run [RUNNUM] 1 1 2 1

The 4th argument is 2, that means the GeneralSort (or the mapping ) will use ../Amrory/GeneralSortTrace.C instead of ../Amory/GeneralSort.C

The 4th argument can be also be more than 2, say, when it is N, it means it will use Proof, a parallel computing framework built-in in root that use N cores.

To display the trace, we can use ../Armory/readTrace.C ( this macro is kind of shitty.....)

= How to count a 1D histogram for a given range ? =

After ./process_run, a function Check1D() is loaded.

= How to fit the excitation spectrum ? =

If the reaction.dat is set properly, after ./process_run, the excite() function will give you the excitation spectrum.

root>excite()

You can use the fitAuto() function to auto fit the spectrum by

root>fitAuto(hEx)

For more option

fitAuto( [hist name], [BG estimation] )

-------------------------------
Or you can can fit N-Gauss + 1 linear function. In this case, edit the AutFit_para.txt

root>fitNGaussP1(hEx)

"How to" for analysis code

2022-03-28T06:46:57Z

Ttang:

[last updated Mar 28, 2022]

Everything should be performed in digios/analysis/working directory,

{| class="wikitable"
|-
|ATTENTION:
|-
|txt file extension is editable for user.
|-
|dat files extension is not supposed to be edited, they are generated.
|-
|Editable file name will be highlighted with blue color
|}

= Overview =

[[File:Screenshot 2022-03-28 023801.png|1200px|frameless]]

= General Usage =

== How to download the source code ? ==

make sure you have git in your computer.

in the directory you like to put in the code. for example, I like to put the code in ~/, then >cd ~/

~/>git clone https://github.com/calemhoffman/digios.git

you will see a folder name digios is there.

digios>cd digios

digios>git status

To check your experiment

digios>git branch -a

for example your experiment is using the branch h064_15N

digios>git status

you will see you are in the branch for your experiment.

for analysis, you only need the things inside digios/analysis

Make sure you create folders or symbolic links for data, merged_data, and root_data under digios/analysis.

== How to get option for a method or function ? ==

For most of the bash script, if you have no argument or the argument is "-help" it will display help message

working>Process_run

working>../Cleopatra/Transfer -help

For most root macro, for example, RDTCutsCreator(),
after typed the first bracket, use tab, it will display the arguments.

root>RDTCutsCreator(

then press tab. it will show

root>RDTCutsCreator(TString filename, TString saveFileName = "rdtCuts.root", int eRange = 4000, int eRange = 60000 )

== How to take a screenshot in MAC ? ==

Command + Shift + 4 = screenshot selected area

Command + Shift + 4, then space_bar = screenshot selected window

== How to check the start time and stop time for a run? ==

in digios/analysis/data, there is RunTimeStamp.dat.
this file stored all start and stop time for all runs.

in MAC or DAQ,

anywhere>ShowRunTimeStamp

== How to check the raw files for a run? ==

in MAC or DAQ

anywhere>ShowRunSize [RUNNUM]

= Git Branch Management =

== How to Setup/Switch for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Has to be done in the DAQ first
|-
|CAUTION: Has to be done in the MAC after
|}

given that the digios directory is clean, meaning

digios>git status

show no file is modified.

If you are not in the master branch

digios>./SetUpNewExp master

Then you are ready to setup a new experimental branch by

digios>./SetUpNewExp [new experiment name]

The bash script with do all the work.

After that, do the same in the MAC.

----------

When the folder is not clean. i.e., not everything git committed. The SetUpNewExp will stop and not switch branches or make a new experiment.

In that case, the simplest way is

digios>git add -A # add all changes to stage
digios>git commit -m "comment you like" # commit the change and make the folder clean

Or, you want to discard all change

digios>git reset --hard

== How to clean up the working directory and prepare for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Need to be done in both MAC and DAQ
|-
|CAUTION: !!! READ till the end before you do anything!!!!
|}

After each experiment, the files in digios directory would be changed.

To check the change,

DAQ>cd ~/digios

digios>git status

To snapshot the change

digios>git add -A
digios>git commit -m "comment for this snapshot"

It is better to push the snapshot to the github

digios>git push origin [branch name]

{| class="wikitable"
|-
|CAUTION: Also need to git the DAQ!
|-
|CAUTION: The files in the DAQ and the MAC could be both changed. Mostly, the change in the DAQ is in digios/daq.
|-
|CAUTION: That means the DAQ and MAC has to be merged.
|}

<s>We use a merge driver that the expName.sh will not be merged. The detail can be found in .gitattribute and git documentation. </s>

It is better to start with the DAQ.
# commit and push the daq/edm/scripts folder
# commit and push the daq/edm/screens (if anything changed)

and then, go to the Mac,
# fetch and merge, since the DAQ pushed latest commit
# commit and push the analysis/Armory/
# commit and push the analysis/Cleopatra
# commit and push the analysis/working

Now, we can go to LCRC ( /lcrc/project/HELIOS/digios )
The LCRC always in master branch.
then we can merge and solve conflict for each commit from the experiment.

After above action, we can go back to the DAQ, and commit the expName.sh, and switch back to master branch or setup a new experiment.

= Process Run online =

== How to process run? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/GEBSort, and
GEBSort>make offline
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

working>Process_RUN [RUNNUM]

The bash script will download run [RUNNUM], merge, event building, GeneralSort (mapping), and Monitors.C

to see more options, ./process_run without any argument

working>Process_RUN
Process_RUN [RunNum] [Merge] [EventBuild] [GeneralSort] [Monitor]"
RunNum = run number / \"lastRun\" "
Merge = 1/0/-1 || 1 = merge, 0 = not merge, -1 = force merge "
EventBld = 2/1/0/-1/-2 || 2 = with Trace"
GenralSort = n/1/0/-1/-n || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker"
Monitors = 2/1/0 || 1 = single run, 2 = using the list in ChainMonitors.C"
10 = single run and post to websrv, 20 = list runs and post to websrv"

**** When feeding trace data to Monitors, the EventBld flag must be 2 or -2."

The working flow of process_run (without Monitor) is

[[File:Process run.png|600px|frameless]]

For data calibration, see [[GUI,_Scripts_And_Analysis_Code#Standard_data_analysis_flow|standard data analysis flow]]

== How to process multiple runs at once ? ==
{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

$./process_MultiRuns [RunNum1] [RunNum2] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to process multiple runs as a slurm job? ==

{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

A slurm job is a job in LCRC. The script will generate the slurm.sh and submit the job to 1 node.

If only merge and build event, only 1 core will be used.
If with GeneralSort, 36 cores will be used.

$./process_Slurm [RunNum1] [RunNum2] [time] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
time = allocate time
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to manually run the Monitors.C for a given run? ==

make sure gen_runXXX.root is generated in digios/analysis/root_data.

working>root ../root_data/gen_runXXX.root

working>gen_tree->Process("Monitors.C+")

== How to "Monitor" multiple runs ? ==

edit ChainMonitors.C 

you can see it use the TChain class.

to add files, for example, add the run 33 to 40, 42, 45, and 50, and I assume the run 33 to 40, 42, and 45 are already downloaded

chain->Add("../root_data/gen_run03[3-9].root");
chain->Add("../root_data/gen_run04[0,2,5].root");
chain->Add("../root_data/gen_run050.root");

Then, in process_run

working>./process_run 50 1 1 1 2

Notice that it will download, merge, build event, and GeneralSort (mapping) for run 50 ONLY.

= How to change the array position ? =

edit the file detectorGeo.txt

== How to Donwload all runs into the Mac ? ==

working>Rsyn_data_from_DAQ.sh

== How to change or add a recoil Cuts ? ==

see [[#How to use RDTCutsCreator ?]]

== How to use RDTCutsCreator ? ==

After ./process_run, the ../Armory/RDTCutsCreator.C will be loaded.

root>RDTCutsCreator( [filename], [save file name], [E range], [dE range] )

The default [save file name] is "rdtCuts.root". If you like to use other [save file name], please correct the TString rdtCutFile in Monitors.C

if something go wrong during the RDTCutsCreator, simply delete the "rdtCuts.root".

There is a way to include multiple files for the RDTCutsCreator

root>RDTCutsCreator("../root_data/gen_run02[3-7].root")

or

root>RDTCutsCreator("../root_data/gen_run02[3,5,7,9].root")

To include more files, we can edit ../Armory/RDTCutsCreator.C

inside the file, manual add the files. To run that script.

working> root

root>.L ../Armory/RDTCutsCreator.C

root>RDTCutCreator("", [save file name], [E range], [dE range] )

= How is the Calibration flow ? =
[[File:DataAnalysis.png|800px|frameless]]

The calibration has few steps:
# Gain-matching with xn to xf
# Gain-matching with xn'+xf to e
# Calibrate e

To do step 1, It is better start with alpha data, because the alpha data is independent of position. By gating on 1 of the alpha peak, then plot the xf vs xn, the gain matching of xn to xf can be easily done. And because we need to gate on the alpha peak, then why not do a calibration on the energy using alpha data? So, in the Cali_xf_xn.C, the program will first calibrate alpha energy, then gate on 1 of the alpha peak to do gain match xn to xf.

To do step 2, we need a gain-matched xn, i.e. xn', so that xn'+xf should be proportional to the raw e.

In order to calibrate the energy, sometimes, alpha calibration is doing a good job, given that the alpha source is a good source. However, we can also calibrate the energy using kinematic E-Z lines. See [["How_to"_for_analysis_code#How to Calibrate reaction data by kinematics ?| How to Calibrate reaction data by kinematics ?]]

== How to Calibrate alpha data ? ==

If statistics for single detector is sufficient, i.e. all peak is clearly identified.

edit the file ChainMonitors.C

working>root AutoCalibrationTrace.C+

select option 0

It will guide you through the process.

-----------------------------

If statistics is not so good, we can use the ../Armory/Cali_e_single.C

== How to Gain matching of xn to xf ? ==

working>root AutoCalibrationTrace.C+

select option 0

First, it will go through energy calibration, it does not need to be good.

Next, select any peak, so that the program will gate on that peak and plot xf vs xn. From there, the xn will gain match xf.

== How to gain match the xn+xf to raw e ? ==

To properly do so, you have to gain-matched xn to xf. Then

working>root AutoCalibrationTrace.C+

select option 1

This has to be NOT alpha run, just any beam run. It will plot the raw e vs xf + xn'.

== How to Calibrate reaction data by kinematics ? ==

( I know It needs more detail )

ONLY for sufficient statistic for individual detector.

edit the file ChainMonitors.C

working>root AutoCalibrationtrace.C+

select option 2

it will guide you through.

---------------
In order to speed up the process, it will create a temp.root. a root file only contain e and z.

User can use ../Armory/Check_e_x.root and create a cut to be used in the Monte-Carlo process.

== How to output a root file only contain physical data ? ==

after the calibration is done, we can edit ChainMonitors.C

and run

working>root AutoCalibrationTrace.C+

Select option 3 to generate the A_gen_runXXX.root

[[File:Option3.png|600px|frameless]]

= Kinematic and DWBA Calculation =

The simplest way is using the Simulation_Helper.C. This is a GUI interface.

working>root Simulation_Helper.C

[[File:Simulation Helper screenshot.png|800px|frameless|none]]

== How to change the calculation for Ex and thetaCM ? ==

edit the file reactionConfig.txt, than recalculate the reaction.dat by running ../Cleopatra/Transfer

working>../Cleopatra/Transfer

== How to change the kinematic E-Z line? ==

see [[#How to simulate the kinematics?]]

The E-Z lines are stored in fxList in transfer.root

In Monitors.C, at the end or Monitors::Terminate().

you can see the fxList.

== How to simulate the kinematics? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|}

edit
* reactionConfig.txt 
* detectorGeo.txt 
* Ex.txt 

Then run
working>../Cleopatra/Transfer

after that, 2 files will be generated, 1) reaction.dat, 2) transfer.root

a tree is inside transfer.root.

you can see the tree branches by

root> tree->Print()

I hope the branch name is self-explained.

In Armory, there is a root macro Check_Transfer.C

working>root '../Armory/Check_Transfer.C("transfer.root")'

The macro load the transfer.root and plot the e-z plot, the recoil, recoil radius vs thetaCM etc...

== How to do DWBA calculation ? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|-
|CAUTION: ONLY IN LINUX, because Ptolemy only work in Linux.
|}

edit the file DWBA, then

working>./Cleopatra example 1 1 1 1 0 [minAng] [maxAng] [angStep]

This will generate the example.in, feed to Ptolemy, output example.out, extract the differential cross section into

* example.Xsec.txt
* example.root

And plot the d.s.c. using example.root

It will also generate example.Ex.txt

For arguments meaning, use Cleopatra without any argument

working>./Cleopatra

== How to do kinematics simulation with DWBA differential cross section ? ==

see [[#How to do DWBA calculation ?]] first.

edit
* reactionConfig.txt 
* detectorGeo.txt 
* example 

Make sure the reaction in the reactionConfig.txt is matching with that in example

working>./Cleopatra example 1 1 1 0 1 0 180 1

The excitation levels is using example.Ex.txt.

The bash script will calculate the DWBA d.s.c. using Cleopatra, then using ../Cleopatra/Transfer to do the simulation.

see [[#How to simulate the kinematics?]]

= How to do trace analysis ? =

updated Feb-12, 2021

simply

working>Process_RUN [RunNum] 1 -2 [number_of_worker] [Option_for_Monitors]

Updated Nov-6, 2019
The GEBSort_nogeb_trace was generated, Simple run ./process_run with option is fine

--------------------------------
First, the GEBSort code has to be recompile by changing the file digios/GEBSort/bin_rcnp.C

in that file, comment out the trace (line ?)

Then, recompile

GEBSort>make offline

Now the gen_runXXX.root will contains trace data.

go back to working directory

working>./process_run [RUNNUM] 1 1 2 1

The 4th argument is 2, that means the GeneralSort (or the mapping ) will use ../Amrory/GeneralSortTrace.C instead of ../Amory/GeneralSort.C

The 4th argument can be also be more than 2, say, when it is N, it means it will use Proof, a parallel computing framework built-in in root that use N cores.

To display the trace, we can use ../Armory/readTrace.C ( this macro is kind of shitty.....)

= How to count a 1D histogram for a given range ? =

After ./process_run, a function Check1D() is loaded.

= How to fit the excitation spectrum ? =

If the reaction.dat is set properly, after ./process_run, the excite() function will give you the excitation spectrum.

root>excite()

You can use the fitAuto() function to auto fit the spectrum by

root>fitAuto(hEx)

For more option

fitAuto( [hist name], [BG estimation] )

-------------------------------
Or you can can fit N-Gauss + 1 linear function. In this case, edit the AutFit_para.txt

root>fitNGaussP1(hEx)

"How to" for analysis code

2022-03-28T06:46:47Z

Ttang:

[ updated July 11, 2019]
[last updated Mar 28, 2022]

Everything should be performed in digios/analysis/working directory,

{| class="wikitable"
|-
|ATTENTION:
|-
|txt file extension is editable for user.
|-
|dat files extension is not supposed to be edited, they are generated.
|-
|Editable file name will be highlighted with blue color
|}

= Overview =

[[File:Screenshot 2022-03-28 023801.png|1200px|frameless]]

= General Usage =

== How to download the source code ? ==

make sure you have git in your computer.

in the directory you like to put in the code. for example, I like to put the code in ~/, then >cd ~/

~/>git clone https://github.com/calemhoffman/digios.git

you will see a folder name digios is there.

digios>cd digios

digios>git status

To check your experiment

digios>git branch -a

for example your experiment is using the branch h064_15N

digios>git status

you will see you are in the branch for your experiment.

for analysis, you only need the things inside digios/analysis

Make sure you create folders or symbolic links for data, merged_data, and root_data under digios/analysis.

== How to get option for a method or function ? ==

For most of the bash script, if you have no argument or the argument is "-help" it will display help message

working>Process_run

working>../Cleopatra/Transfer -help

For most root macro, for example, RDTCutsCreator(),
after typed the first bracket, use tab, it will display the arguments.

root>RDTCutsCreator(

then press tab. it will show

root>RDTCutsCreator(TString filename, TString saveFileName = "rdtCuts.root", int eRange = 4000, int eRange = 60000 )

== How to take a screenshot in MAC ? ==

Command + Shift + 4 = screenshot selected area

Command + Shift + 4, then space_bar = screenshot selected window

== How to check the start time and stop time for a run? ==

in digios/analysis/data, there is RunTimeStamp.dat.
this file stored all start and stop time for all runs.

in MAC or DAQ,

anywhere>ShowRunTimeStamp

== How to check the raw files for a run? ==

in MAC or DAQ

anywhere>ShowRunSize [RUNNUM]

= Git Branch Management =

== How to Setup/Switch for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Has to be done in the DAQ first
|-
|CAUTION: Has to be done in the MAC after
|}

given that the digios directory is clean, meaning

digios>git status

show no file is modified.

If you are not in the master branch

digios>./SetUpNewExp master

Then you are ready to setup a new experimental branch by

digios>./SetUpNewExp [new experiment name]

The bash script with do all the work.

After that, do the same in the MAC.

----------

When the folder is not clean. i.e., not everything git committed. The SetUpNewExp will stop and not switch branches or make a new experiment.

In that case, the simplest way is

digios>git add -A # add all changes to stage
digios>git commit -m "comment you like" # commit the change and make the folder clean

Or, you want to discard all change

digios>git reset --hard

== How to clean up the working directory and prepare for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Need to be done in both MAC and DAQ
|-
|CAUTION: !!! READ till the end before you do anything!!!!
|}

After each experiment, the files in digios directory would be changed.

To check the change,

DAQ>cd ~/digios

digios>git status

To snapshot the change

digios>git add -A
digios>git commit -m "comment for this snapshot"

It is better to push the snapshot to the github

digios>git push origin [branch name]

{| class="wikitable"
|-
|CAUTION: Also need to git the DAQ!
|-
|CAUTION: The files in the DAQ and the MAC could be both changed. Mostly, the change in the DAQ is in digios/daq.
|-
|CAUTION: That means the DAQ and MAC has to be merged.
|}

<s>We use a merge driver that the expName.sh will not be merged. The detail can be found in .gitattribute and git documentation. </s>

It is better to start with the DAQ.
# commit and push the daq/edm/scripts folder
# commit and push the daq/edm/screens (if anything changed)

and then, go to the Mac,
# fetch and merge, since the DAQ pushed latest commit
# commit and push the analysis/Armory/
# commit and push the analysis/Cleopatra
# commit and push the analysis/working

Now, we can go to LCRC ( /lcrc/project/HELIOS/digios )
The LCRC always in master branch.
then we can merge and solve conflict for each commit from the experiment.

After above action, we can go back to the DAQ, and commit the expName.sh, and switch back to master branch or setup a new experiment.

= Process Run online =

== How to process run? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/GEBSort, and
GEBSort>make offline
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

working>Process_RUN [RUNNUM]

The bash script will download run [RUNNUM], merge, event building, GeneralSort (mapping), and Monitors.C

to see more options, ./process_run without any argument

working>Process_RUN
Process_RUN [RunNum] [Merge] [EventBuild] [GeneralSort] [Monitor]"
RunNum = run number / \"lastRun\" "
Merge = 1/0/-1 || 1 = merge, 0 = not merge, -1 = force merge "
EventBld = 2/1/0/-1/-2 || 2 = with Trace"
GenralSort = n/1/0/-1/-n || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker"
Monitors = 2/1/0 || 1 = single run, 2 = using the list in ChainMonitors.C"
10 = single run and post to websrv, 20 = list runs and post to websrv"

**** When feeding trace data to Monitors, the EventBld flag must be 2 or -2."

The working flow of process_run (without Monitor) is

[[File:Process run.png|600px|frameless]]

For data calibration, see [[GUI,_Scripts_And_Analysis_Code#Standard_data_analysis_flow|standard data analysis flow]]

== How to process multiple runs at once ? ==
{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

$./process_MultiRuns [RunNum1] [RunNum2] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to process multiple runs as a slurm job? ==

{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

A slurm job is a job in LCRC. The script will generate the slurm.sh and submit the job to 1 node.

If only merge and build event, only 1 core will be used.
If with GeneralSort, 36 cores will be used.

$./process_Slurm [RunNum1] [RunNum2] [time] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
time = allocate time
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to manually run the Monitors.C for a given run? ==

make sure gen_runXXX.root is generated in digios/analysis/root_data.

working>root ../root_data/gen_runXXX.root

working>gen_tree->Process("Monitors.C+")

== How to "Monitor" multiple runs ? ==

edit ChainMonitors.C 

you can see it use the TChain class.

to add files, for example, add the run 33 to 40, 42, 45, and 50, and I assume the run 33 to 40, 42, and 45 are already downloaded

chain->Add("../root_data/gen_run03[3-9].root");
chain->Add("../root_data/gen_run04[0,2,5].root");
chain->Add("../root_data/gen_run050.root");

Then, in process_run

working>./process_run 50 1 1 1 2

Notice that it will download, merge, build event, and GeneralSort (mapping) for run 50 ONLY.

= How to change the array position ? =

edit the file detectorGeo.txt

== How to Donwload all runs into the Mac ? ==

working>Rsyn_data_from_DAQ.sh

== How to change or add a recoil Cuts ? ==

see [[#How to use RDTCutsCreator ?]]

== How to use RDTCutsCreator ? ==

After ./process_run, the ../Armory/RDTCutsCreator.C will be loaded.

root>RDTCutsCreator( [filename], [save file name], [E range], [dE range] )

The default [save file name] is "rdtCuts.root". If you like to use other [save file name], please correct the TString rdtCutFile in Monitors.C

if something go wrong during the RDTCutsCreator, simply delete the "rdtCuts.root".

There is a way to include multiple files for the RDTCutsCreator

root>RDTCutsCreator("../root_data/gen_run02[3-7].root")

or

root>RDTCutsCreator("../root_data/gen_run02[3,5,7,9].root")

To include more files, we can edit ../Armory/RDTCutsCreator.C

inside the file, manual add the files. To run that script.

working> root

root>.L ../Armory/RDTCutsCreator.C

root>RDTCutCreator("", [save file name], [E range], [dE range] )

= How is the Calibration flow ? =
[[File:DataAnalysis.png|800px|frameless]]

The calibration has few steps:
# Gain-matching with xn to xf
# Gain-matching with xn'+xf to e
# Calibrate e

To do step 1, It is better start with alpha data, because the alpha data is independent of position. By gating on 1 of the alpha peak, then plot the xf vs xn, the gain matching of xn to xf can be easily done. And because we need to gate on the alpha peak, then why not do a calibration on the energy using alpha data? So, in the Cali_xf_xn.C, the program will first calibrate alpha energy, then gate on 1 of the alpha peak to do gain match xn to xf.

To do step 2, we need a gain-matched xn, i.e. xn', so that xn'+xf should be proportional to the raw e.

In order to calibrate the energy, sometimes, alpha calibration is doing a good job, given that the alpha source is a good source. However, we can also calibrate the energy using kinematic E-Z lines. See [["How_to"_for_analysis_code#How to Calibrate reaction data by kinematics ?| How to Calibrate reaction data by kinematics ?]]

== How to Calibrate alpha data ? ==

If statistics for single detector is sufficient, i.e. all peak is clearly identified.

edit the file ChainMonitors.C

working>root AutoCalibrationTrace.C+

select option 0

It will guide you through the process.

-----------------------------

If statistics is not so good, we can use the ../Armory/Cali_e_single.C

== How to Gain matching of xn to xf ? ==

working>root AutoCalibrationTrace.C+

select option 0

First, it will go through energy calibration, it does not need to be good.

Next, select any peak, so that the program will gate on that peak and plot xf vs xn. From there, the xn will gain match xf.

== How to gain match the xn+xf to raw e ? ==

To properly do so, you have to gain-matched xn to xf. Then

working>root AutoCalibrationTrace.C+

select option 1

This has to be NOT alpha run, just any beam run. It will plot the raw e vs xf + xn'.

== How to Calibrate reaction data by kinematics ? ==

( I know It needs more detail )

ONLY for sufficient statistic for individual detector.

edit the file ChainMonitors.C

working>root AutoCalibrationtrace.C+

select option 2

it will guide you through.

---------------
In order to speed up the process, it will create a temp.root. a root file only contain e and z.

User can use ../Armory/Check_e_x.root and create a cut to be used in the Monte-Carlo process.

== How to output a root file only contain physical data ? ==

after the calibration is done, we can edit ChainMonitors.C

and run

working>root AutoCalibrationTrace.C+

Select option 3 to generate the A_gen_runXXX.root

[[File:Option3.png|600px|frameless]]

= Kinematic and DWBA Calculation =

The simplest way is using the Simulation_Helper.C. This is a GUI interface.

working>root Simulation_Helper.C

[[File:Simulation Helper screenshot.png|800px|frameless|none]]

== How to change the calculation for Ex and thetaCM ? ==

edit the file reactionConfig.txt, than recalculate the reaction.dat by running ../Cleopatra/Transfer

working>../Cleopatra/Transfer

== How to change the kinematic E-Z line? ==

see [[#How to simulate the kinematics?]]

The E-Z lines are stored in fxList in transfer.root

In Monitors.C, at the end or Monitors::Terminate().

you can see the fxList.

== How to simulate the kinematics? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|}

edit
* reactionConfig.txt 
* detectorGeo.txt 
* Ex.txt 

Then run
working>../Cleopatra/Transfer

after that, 2 files will be generated, 1) reaction.dat, 2) transfer.root

a tree is inside transfer.root.

you can see the tree branches by

root> tree->Print()

I hope the branch name is self-explained.

In Armory, there is a root macro Check_Transfer.C

working>root '../Armory/Check_Transfer.C("transfer.root")'

The macro load the transfer.root and plot the e-z plot, the recoil, recoil radius vs thetaCM etc...

== How to do DWBA calculation ? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|-
|CAUTION: ONLY IN LINUX, because Ptolemy only work in Linux.
|}

edit the file DWBA, then

working>./Cleopatra example 1 1 1 1 0 [minAng] [maxAng] [angStep]

This will generate the example.in, feed to Ptolemy, output example.out, extract the differential cross section into

* example.Xsec.txt
* example.root

And plot the d.s.c. using example.root

It will also generate example.Ex.txt

For arguments meaning, use Cleopatra without any argument

working>./Cleopatra

== How to do kinematics simulation with DWBA differential cross section ? ==

see [[#How to do DWBA calculation ?]] first.

edit
* reactionConfig.txt 
* detectorGeo.txt 
* example 

Make sure the reaction in the reactionConfig.txt is matching with that in example

working>./Cleopatra example 1 1 1 0 1 0 180 1

The excitation levels is using example.Ex.txt.

The bash script will calculate the DWBA d.s.c. using Cleopatra, then using ../Cleopatra/Transfer to do the simulation.

see [[#How to simulate the kinematics?]]

= How to do trace analysis ? =

updated Feb-12, 2021

simply

working>Process_RUN [RunNum] 1 -2 [number_of_worker] [Option_for_Monitors]

Updated Nov-6, 2019
The GEBSort_nogeb_trace was generated, Simple run ./process_run with option is fine

--------------------------------
First, the GEBSort code has to be recompile by changing the file digios/GEBSort/bin_rcnp.C

in that file, comment out the trace (line ?)

Then, recompile

GEBSort>make offline

Now the gen_runXXX.root will contains trace data.

go back to working directory

working>./process_run [RUNNUM] 1 1 2 1

The 4th argument is 2, that means the GeneralSort (or the mapping ) will use ../Amrory/GeneralSortTrace.C instead of ../Amory/GeneralSort.C

The 4th argument can be also be more than 2, say, when it is N, it means it will use Proof, a parallel computing framework built-in in root that use N cores.

To display the trace, we can use ../Armory/readTrace.C ( this macro is kind of shitty.....)

= How to count a 1D histogram for a given range ? =

After ./process_run, a function Check1D() is loaded.

= How to fit the excitation spectrum ? =

If the reaction.dat is set properly, after ./process_run, the excite() function will give you the excitation spectrum.

root>excite()

You can use the fitAuto() function to auto fit the spectrum by

root>fitAuto(hEx)

For more option

fitAuto( [hist name], [BG estimation] )

-------------------------------
Or you can can fit N-Gauss + 1 linear function. In this case, edit the AutFit_para.txt

root>fitNGaussP1(hEx)

"How to" for analysis code

2022-03-28T06:39:18Z

Ttang: /* Overview */

[last updated July 11, 2019]

Everything should be performed in digios/analysis/working directory,

{| class="wikitable"
|-
|ATTENTION:
|-
|txt file extension is editable for user.
|-
|dat files extension is not supposed to be edited, they are generated.
|-
|Editable file name will be highlighted with blue color
|}

= Overview =

[[File:Screenshot 2022-03-28 023801.png|1200px|frameless]]

= General Usage =

== How to download the source code ? ==

make sure you have git in your computer.

in the directory you like to put in the code. for example, I like to put the code in ~/, then >cd ~/

~/>git clone https://github.com/calemhoffman/digios.git

you will see a folder name digios is there.

digios>cd digios

digios>git status

To check your experiment

digios>git branch -a

for example your experiment is using the branch h064_15N

digios>git status

you will see you are in the branch for your experiment.

for analysis, you only need the things inside digios/analysis

Make sure you create folders or symbolic links for data, merged_data, and root_data under digios/analysis.

== How to get option for a method or function ? ==

For most of the bash script, if you have no argument or the argument is "-help" it will display help message

working>Process_run

working>../Cleopatra/Transfer -help

For most root macro, for example, RDTCutsCreator(),
after typed the first bracket, use tab, it will display the arguments.

root>RDTCutsCreator(

then press tab. it will show

root>RDTCutsCreator(TString filename, TString saveFileName = "rdtCuts.root", int eRange = 4000, int eRange = 60000 )

== How to take a screenshot in MAC ? ==

Command + Shift + 4 = screenshot selected area

Command + Shift + 4, then space_bar = screenshot selected window

== How to check the start time and stop time for a run? ==

in digios/analysis/data, there is RunTimeStamp.dat.
this file stored all start and stop time for all runs.

in MAC or DAQ,

anywhere>ShowRunTimeStamp

== How to check the raw files for a run? ==

in MAC or DAQ

anywhere>ShowRunSize [RUNNUM]

= Git Branch Management =

== How to Setup/Switch for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Has to be done in the DAQ first
|-
|CAUTION: Has to be done in the MAC after
|}

given that the digios directory is clean, meaning

digios>git status

show no file is modified.

If you are not in the master branch

digios>./SetUpNewExp master

Then you are ready to setup a new experimental branch by

digios>./SetUpNewExp [new experiment name]

The bash script with do all the work.

After that, do the same in the MAC.

----------

When the folder is not clean. i.e., not everything git committed. The SetUpNewExp will stop and not switch branches or make a new experiment.

In that case, the simplest way is

digios>git add -A # add all changes to stage
digios>git commit -m "comment you like" # commit the change and make the folder clean

Or, you want to discard all change

digios>git reset --hard

== How to clean up the working directory and prepare for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Need to be done in both MAC and DAQ
|-
|CAUTION: !!! READ till the end before you do anything!!!!
|}

After each experiment, the files in digios directory would be changed.

To check the change,

DAQ>cd ~/digios

digios>git status

To snapshot the change

digios>git add -A
digios>git commit -m "comment for this snapshot"

It is better to push the snapshot to the github

digios>git push origin [branch name]

{| class="wikitable"
|-
|CAUTION: Also need to git the DAQ!
|-
|CAUTION: The files in the DAQ and the MAC could be both changed. Mostly, the change in the DAQ is in digios/daq.
|-
|CAUTION: That means the DAQ and MAC has to be merged.
|}

<s>We use a merge driver that the expName.sh will not be merged. The detail can be found in .gitattribute and git documentation. </s>

It is better to start with the DAQ.
# commit and push the daq/edm/scripts folder
# commit and push the daq/edm/screens (if anything changed)

and then, go to the Mac,
# fetch and merge, since the DAQ pushed latest commit
# commit and push the analysis/Armory/
# commit and push the analysis/Cleopatra
# commit and push the analysis/working

Now, we can go to LCRC ( /lcrc/project/HELIOS/digios )
The LCRC always in master branch.
then we can merge and solve conflict for each commit from the experiment.

After above action, we can go back to the DAQ, and commit the expName.sh, and switch back to master branch or setup a new experiment.

= Process Run online =

== How to process run? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/GEBSort, and
GEBSort>make offline
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

working>Process_RUN [RUNNUM]

The bash script will download run [RUNNUM], merge, event building, GeneralSort (mapping), and Monitors.C

to see more options, ./process_run without any argument

working>Process_RUN
Process_RUN [RunNum] [Merge] [EventBuild] [GeneralSort] [Monitor]"
RunNum = run number / \"lastRun\" "
Merge = 1/0/-1 || 1 = merge, 0 = not merge, -1 = force merge "
EventBld = 2/1/0/-1/-2 || 2 = with Trace"
GenralSort = n/1/0/-1/-n || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker"
Monitors = 2/1/0 || 1 = single run, 2 = using the list in ChainMonitors.C"
10 = single run and post to websrv, 20 = list runs and post to websrv"

**** When feeding trace data to Monitors, the EventBld flag must be 2 or -2."

The working flow of process_run (without Monitor) is

[[File:Process run.png|600px|frameless]]

For data calibration, see [[GUI,_Scripts_And_Analysis_Code#Standard_data_analysis_flow|standard data analysis flow]]

== How to process multiple runs at once ? ==
{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

$./process_MultiRuns [RunNum1] [RunNum2] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to process multiple runs as a slurm job? ==

{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

A slurm job is a job in LCRC. The script will generate the slurm.sh and submit the job to 1 node.

If only merge and build event, only 1 core will be used.
If with GeneralSort, 36 cores will be used.

$./process_Slurm [RunNum1] [RunNum2] [time] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
time = allocate time
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to manually run the Monitors.C for a given run? ==

make sure gen_runXXX.root is generated in digios/analysis/root_data.

working>root ../root_data/gen_runXXX.root

working>gen_tree->Process("Monitors.C+")

== How to "Monitor" multiple runs ? ==

edit ChainMonitors.C 

you can see it use the TChain class.

to add files, for example, add the run 33 to 40, 42, 45, and 50, and I assume the run 33 to 40, 42, and 45 are already downloaded

chain->Add("../root_data/gen_run03[3-9].root");
chain->Add("../root_data/gen_run04[0,2,5].root");
chain->Add("../root_data/gen_run050.root");

Then, in process_run

working>./process_run 50 1 1 1 2

Notice that it will download, merge, build event, and GeneralSort (mapping) for run 50 ONLY.

= How to change the array position ? =

edit the file detectorGeo.txt

== How to Donwload all runs into the Mac ? ==

working>Rsyn_data_from_DAQ.sh

== How to change or add a recoil Cuts ? ==

see [[#How to use RDTCutsCreator ?]]

== How to use RDTCutsCreator ? ==

After ./process_run, the ../Armory/RDTCutsCreator.C will be loaded.

root>RDTCutsCreator( [filename], [save file name], [E range], [dE range] )

The default [save file name] is "rdtCuts.root". If you like to use other [save file name], please correct the TString rdtCutFile in Monitors.C

if something go wrong during the RDTCutsCreator, simply delete the "rdtCuts.root".

There is a way to include multiple files for the RDTCutsCreator

root>RDTCutsCreator("../root_data/gen_run02[3-7].root")

or

root>RDTCutsCreator("../root_data/gen_run02[3,5,7,9].root")

To include more files, we can edit ../Armory/RDTCutsCreator.C

inside the file, manual add the files. To run that script.

working> root

root>.L ../Armory/RDTCutsCreator.C

root>RDTCutCreator("", [save file name], [E range], [dE range] )

= How is the Calibration flow ? =
[[File:DataAnalysis.png|800px|frameless]]

The calibration has few steps:
# Gain-matching with xn to xf
# Gain-matching with xn'+xf to e
# Calibrate e

To do step 1, It is better start with alpha data, because the alpha data is independent of position. By gating on 1 of the alpha peak, then plot the xf vs xn, the gain matching of xn to xf can be easily done. And because we need to gate on the alpha peak, then why not do a calibration on the energy using alpha data? So, in the Cali_xf_xn.C, the program will first calibrate alpha energy, then gate on 1 of the alpha peak to do gain match xn to xf.

To do step 2, we need a gain-matched xn, i.e. xn', so that xn'+xf should be proportional to the raw e.

In order to calibrate the energy, sometimes, alpha calibration is doing a good job, given that the alpha source is a good source. However, we can also calibrate the energy using kinematic E-Z lines. See [["How_to"_for_analysis_code#How to Calibrate reaction data by kinematics ?| How to Calibrate reaction data by kinematics ?]]

== How to Calibrate alpha data ? ==

If statistics for single detector is sufficient, i.e. all peak is clearly identified.

edit the file ChainMonitors.C

working>root AutoCalibrationTrace.C+

select option 0

It will guide you through the process.

-----------------------------

If statistics is not so good, we can use the ../Armory/Cali_e_single.C

== How to Gain matching of xn to xf ? ==

working>root AutoCalibrationTrace.C+

select option 0

First, it will go through energy calibration, it does not need to be good.

Next, select any peak, so that the program will gate on that peak and plot xf vs xn. From there, the xn will gain match xf.

== How to gain match the xn+xf to raw e ? ==

To properly do so, you have to gain-matched xn to xf. Then

working>root AutoCalibrationTrace.C+

select option 1

This has to be NOT alpha run, just any beam run. It will plot the raw e vs xf + xn'.

== How to Calibrate reaction data by kinematics ? ==

( I know It needs more detail )

ONLY for sufficient statistic for individual detector.

edit the file ChainMonitors.C

working>root AutoCalibrationtrace.C+

select option 2

it will guide you through.

---------------
In order to speed up the process, it will create a temp.root. a root file only contain e and z.

User can use ../Armory/Check_e_x.root and create a cut to be used in the Monte-Carlo process.

== How to output a root file only contain physical data ? ==

after the calibration is done, we can edit ChainMonitors.C

and run

working>root AutoCalibrationTrace.C+

Select option 3 to generate the A_gen_runXXX.root

[[File:Option3.png|600px|frameless]]

= Kinematic and DWBA Calculation =

The simplest way is using the Simulation_Helper.C. This is a GUI interface.

working>root Simulation_Helper.C

[[File:Simulation Helper screenshot.png|800px|frameless|none]]

== How to change the calculation for Ex and thetaCM ? ==

edit the file reactionConfig.txt, than recalculate the reaction.dat by running ../Cleopatra/Transfer

working>../Cleopatra/Transfer

== How to change the kinematic E-Z line? ==

see [[#How to simulate the kinematics?]]

The E-Z lines are stored in fxList in transfer.root

In Monitors.C, at the end or Monitors::Terminate().

you can see the fxList.

== How to simulate the kinematics? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|}

edit
* reactionConfig.txt 
* detectorGeo.txt 
* Ex.txt 

Then run
working>../Cleopatra/Transfer

after that, 2 files will be generated, 1) reaction.dat, 2) transfer.root

a tree is inside transfer.root.

you can see the tree branches by

root> tree->Print()

I hope the branch name is self-explained.

In Armory, there is a root macro Check_Transfer.C

working>root '../Armory/Check_Transfer.C("transfer.root")'

The macro load the transfer.root and plot the e-z plot, the recoil, recoil radius vs thetaCM etc...

== How to do DWBA calculation ? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|-
|CAUTION: ONLY IN LINUX, because Ptolemy only work in Linux.
|}

edit the file DWBA, then

working>./Cleopatra example 1 1 1 1 0 [minAng] [maxAng] [angStep]

This will generate the example.in, feed to Ptolemy, output example.out, extract the differential cross section into

* example.Xsec.txt
* example.root

And plot the d.s.c. using example.root

It will also generate example.Ex.txt

For arguments meaning, use Cleopatra without any argument

working>./Cleopatra

== How to do kinematics simulation with DWBA differential cross section ? ==

see [[#How to do DWBA calculation ?]] first.

edit
* reactionConfig.txt 
* detectorGeo.txt 
* example 

Make sure the reaction in the reactionConfig.txt is matching with that in example

working>./Cleopatra example 1 1 1 0 1 0 180 1

The excitation levels is using example.Ex.txt.

The bash script will calculate the DWBA d.s.c. using Cleopatra, then using ../Cleopatra/Transfer to do the simulation.

see [[#How to simulate the kinematics?]]

= How to do trace analysis ? =

updated Feb-12, 2021

simply

working>Process_RUN [RunNum] 1 -2 [number_of_worker] [Option_for_Monitors]

Updated Nov-6, 2019
The GEBSort_nogeb_trace was generated, Simple run ./process_run with option is fine

--------------------------------
First, the GEBSort code has to be recompile by changing the file digios/GEBSort/bin_rcnp.C

in that file, comment out the trace (line ?)

Then, recompile

GEBSort>make offline

Now the gen_runXXX.root will contains trace data.

go back to working directory

working>./process_run [RUNNUM] 1 1 2 1

The 4th argument is 2, that means the GeneralSort (or the mapping ) will use ../Amrory/GeneralSortTrace.C instead of ../Amory/GeneralSort.C

The 4th argument can be also be more than 2, say, when it is N, it means it will use Proof, a parallel computing framework built-in in root that use N cores.

To display the trace, we can use ../Armory/readTrace.C ( this macro is kind of shitty.....)

= How to count a 1D histogram for a given range ? =

After ./process_run, a function Check1D() is loaded.

= How to fit the excitation spectrum ? =

If the reaction.dat is set properly, after ./process_run, the excite() function will give you the excitation spectrum.

root>excite()

You can use the fitAuto() function to auto fit the spectrum by

root>fitAuto(hEx)

For more option

fitAuto( [hist name], [BG estimation] )

-------------------------------
Or you can can fit N-Gauss + 1 linear function. In this case, edit the AutFit_para.txt

root>fitNGaussP1(hEx)

File:Screenshot 2022-03-28 023801.png

2022-03-28T06:38:47Z

Ttang:

Flow of data analysis

"How to" for analysis code

2022-03-28T06:36:06Z

Ttang: /* General Flow */

[last updated July 11, 2019]

Everything should be performed in digios/analysis/working directory,

{| class="wikitable"
|-
|ATTENTION:
|-
|txt file extension is editable for user.
|-
|dat files extension is not supposed to be edited, they are generated.
|-
|Editable file name will be highlighted with blue color
|}

= Overview =
[[File:Digios analysis.png|1000px|frameless]]

= General Usage =

== How to download the source code ? ==

make sure you have git in your computer.

in the directory you like to put in the code. for example, I like to put the code in ~/, then >cd ~/

~/>git clone https://github.com/calemhoffman/digios.git

you will see a folder name digios is there.

digios>cd digios

digios>git status

To check your experiment

digios>git branch -a

for example your experiment is using the branch h064_15N

digios>git status

you will see you are in the branch for your experiment.

for analysis, you only need the things inside digios/analysis

Make sure you create folders or symbolic links for data, merged_data, and root_data under digios/analysis.

== How to get option for a method or function ? ==

For most of the bash script, if you have no argument or the argument is "-help" it will display help message

working>Process_run

working>../Cleopatra/Transfer -help

For most root macro, for example, RDTCutsCreator(),
after typed the first bracket, use tab, it will display the arguments.

root>RDTCutsCreator(

then press tab. it will show

root>RDTCutsCreator(TString filename, TString saveFileName = "rdtCuts.root", int eRange = 4000, int eRange = 60000 )

== How to take a screenshot in MAC ? ==

Command + Shift + 4 = screenshot selected area

Command + Shift + 4, then space_bar = screenshot selected window

== How to check the start time and stop time for a run? ==

in digios/analysis/data, there is RunTimeStamp.dat.
this file stored all start and stop time for all runs.

in MAC or DAQ,

anywhere>ShowRunTimeStamp

== How to check the raw files for a run? ==

in MAC or DAQ

anywhere>ShowRunSize [RUNNUM]

= Git Branch Management =

== How to Setup/Switch for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Has to be done in the DAQ first
|-
|CAUTION: Has to be done in the MAC after
|}

given that the digios directory is clean, meaning

digios>git status

show no file is modified.

If you are not in the master branch

digios>./SetUpNewExp master

Then you are ready to setup a new experimental branch by

digios>./SetUpNewExp [new experiment name]

The bash script with do all the work.

After that, do the same in the MAC.

----------

When the folder is not clean. i.e., not everything git committed. The SetUpNewExp will stop and not switch branches or make a new experiment.

In that case, the simplest way is

digios>git add -A # add all changes to stage
digios>git commit -m "comment you like" # commit the change and make the folder clean

Or, you want to discard all change

digios>git reset --hard

== How to clean up the working directory and prepare for a new experiment? ==

{| class="wikitable"
|-
|CAUTION: Advance user / user familiar with git only
|-
|CAUTION: Need to be done in both MAC and DAQ
|-
|CAUTION: !!! READ till the end before you do anything!!!!
|}

After each experiment, the files in digios directory would be changed.

To check the change,

DAQ>cd ~/digios

digios>git status

To snapshot the change

digios>git add -A
digios>git commit -m "comment for this snapshot"

It is better to push the snapshot to the github

digios>git push origin [branch name]

{| class="wikitable"
|-
|CAUTION: Also need to git the DAQ!
|-
|CAUTION: The files in the DAQ and the MAC could be both changed. Mostly, the change in the DAQ is in digios/daq.
|-
|CAUTION: That means the DAQ and MAC has to be merged.
|}

<s>We use a merge driver that the expName.sh will not be merged. The detail can be found in .gitattribute and git documentation. </s>

It is better to start with the DAQ.
# commit and push the daq/edm/scripts folder
# commit and push the daq/edm/screens (if anything changed)

and then, go to the Mac,
# fetch and merge, since the DAQ pushed latest commit
# commit and push the analysis/Armory/
# commit and push the analysis/Cleopatra
# commit and push the analysis/working

Now, we can go to LCRC ( /lcrc/project/HELIOS/digios )
The LCRC always in master branch.
then we can merge and solve conflict for each commit from the experiment.

After above action, we can go back to the DAQ, and commit the expName.sh, and switch back to master branch or setup a new experiment.

= Process Run online =

== How to process run? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/GEBSort, and
GEBSort>make offline
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

working>Process_RUN [RUNNUM]

The bash script will download run [RUNNUM], merge, event building, GeneralSort (mapping), and Monitors.C

to see more options, ./process_run without any argument

working>Process_RUN
Process_RUN [RunNum] [Merge] [EventBuild] [GeneralSort] [Monitor]"
RunNum = run number / \"lastRun\" "
Merge = 1/0/-1 || 1 = merge, 0 = not merge, -1 = force merge "
EventBld = 2/1/0/-1/-2 || 2 = with Trace"
GenralSort = n/1/0/-1/-n || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker"
Monitors = 2/1/0 || 1 = single run, 2 = using the list in ChainMonitors.C"
10 = single run and post to websrv, 20 = list runs and post to websrv"

**** When feeding trace data to Monitors, the EventBld flag must be 2 or -2."

The working flow of process_run (without Monitor) is

[[File:Process run.png|600px|frameless]]

For data calibration, see [[GUI,_Scripts_And_Analysis_Code#Standard_data_analysis_flow|standard data analysis flow]]

== How to process multiple runs at once ? ==
{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

$./process_MultiRuns [RunNum1] [RunNum2] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to process multiple runs as a slurm job? ==

{| class="wikitable"
|-
|CAUTION: In case of trace analysis, Please edit the GeneralSortMapping.h path in digios/analysis/Armory/GeneralSortTraceProof.C
|}

A slurm job is a job in LCRC. The script will generate the slurm.sh and submit the job to 1 node.

If only merge and build event, only 1 core will be used.
If with GeneralSort, 36 cores will be used.

$./process_Slurm [RunNum1] [RunNum2] [time] [Merge] [EventBuild] [GeneralSort]
RunNum1 = start run number
RunNum2 = stop run number
time = allocate time
Merge = 1/0*
EventBld = 2/1/0* || 2 = with Trace
GenralSort = n/1/0* || 1 = GeneralSort.C, n = GeneralSortTraceProof.C with n-worker
* negative option = force

== How to manually run the Monitors.C for a given run? ==

make sure gen_runXXX.root is generated in digios/analysis/root_data.

working>root ../root_data/gen_runXXX.root

working>gen_tree->Process("Monitors.C+")

== How to "Monitor" multiple runs ? ==

edit ChainMonitors.C 

you can see it use the TChain class.

to add files, for example, add the run 33 to 40, 42, 45, and 50, and I assume the run 33 to 40, 42, and 45 are already downloaded

chain->Add("../root_data/gen_run03[3-9].root");
chain->Add("../root_data/gen_run04[0,2,5].root");
chain->Add("../root_data/gen_run050.root");

Then, in process_run

working>./process_run 50 1 1 1 2

Notice that it will download, merge, build event, and GeneralSort (mapping) for run 50 ONLY.

= How to change the array position ? =

edit the file detectorGeo.txt

== How to Donwload all runs into the Mac ? ==

working>Rsyn_data_from_DAQ.sh

== How to change or add a recoil Cuts ? ==

see [[#How to use RDTCutsCreator ?]]

== How to use RDTCutsCreator ? ==

After ./process_run, the ../Armory/RDTCutsCreator.C will be loaded.

root>RDTCutsCreator( [filename], [save file name], [E range], [dE range] )

The default [save file name] is "rdtCuts.root". If you like to use other [save file name], please correct the TString rdtCutFile in Monitors.C

if something go wrong during the RDTCutsCreator, simply delete the "rdtCuts.root".

There is a way to include multiple files for the RDTCutsCreator

root>RDTCutsCreator("../root_data/gen_run02[3-7].root")

or

root>RDTCutsCreator("../root_data/gen_run02[3,5,7,9].root")

To include more files, we can edit ../Armory/RDTCutsCreator.C

inside the file, manual add the files. To run that script.

working> root

root>.L ../Armory/RDTCutsCreator.C

root>RDTCutCreator("", [save file name], [E range], [dE range] )

= How is the Calibration flow ? =
[[File:DataAnalysis.png|800px|frameless]]

The calibration has few steps:
# Gain-matching with xn to xf
# Gain-matching with xn'+xf to e
# Calibrate e

To do step 1, It is better start with alpha data, because the alpha data is independent of position. By gating on 1 of the alpha peak, then plot the xf vs xn, the gain matching of xn to xf can be easily done. And because we need to gate on the alpha peak, then why not do a calibration on the energy using alpha data? So, in the Cali_xf_xn.C, the program will first calibrate alpha energy, then gate on 1 of the alpha peak to do gain match xn to xf.

To do step 2, we need a gain-matched xn, i.e. xn', so that xn'+xf should be proportional to the raw e.

In order to calibrate the energy, sometimes, alpha calibration is doing a good job, given that the alpha source is a good source. However, we can also calibrate the energy using kinematic E-Z lines. See [["How_to"_for_analysis_code#How to Calibrate reaction data by kinematics ?| How to Calibrate reaction data by kinematics ?]]

== How to Calibrate alpha data ? ==

If statistics for single detector is sufficient, i.e. all peak is clearly identified.

edit the file ChainMonitors.C

working>root AutoCalibrationTrace.C+

select option 0

It will guide you through the process.

-----------------------------

If statistics is not so good, we can use the ../Armory/Cali_e_single.C

== How to Gain matching of xn to xf ? ==

working>root AutoCalibrationTrace.C+

select option 0

First, it will go through energy calibration, it does not need to be good.

Next, select any peak, so that the program will gate on that peak and plot xf vs xn. From there, the xn will gain match xf.

== How to gain match the xn+xf to raw e ? ==

To properly do so, you have to gain-matched xn to xf. Then

working>root AutoCalibrationTrace.C+

select option 1

This has to be NOT alpha run, just any beam run. It will plot the raw e vs xf + xn'.

== How to Calibrate reaction data by kinematics ? ==

( I know It needs more detail )

ONLY for sufficient statistic for individual detector.

edit the file ChainMonitors.C

working>root AutoCalibrationtrace.C+

select option 2

it will guide you through.

---------------
In order to speed up the process, it will create a temp.root. a root file only contain e and z.

User can use ../Armory/Check_e_x.root and create a cut to be used in the Monte-Carlo process.

== How to output a root file only contain physical data ? ==

after the calibration is done, we can edit ChainMonitors.C

and run

working>root AutoCalibrationTrace.C+

Select option 3 to generate the A_gen_runXXX.root

[[File:Option3.png|600px|frameless]]

= Kinematic and DWBA Calculation =

The simplest way is using the Simulation_Helper.C. This is a GUI interface.

working>root Simulation_Helper.C

[[File:Simulation Helper screenshot.png|800px|frameless|none]]

== How to change the calculation for Ex and thetaCM ? ==

edit the file reactionConfig.txt, than recalculate the reaction.dat by running ../Cleopatra/Transfer

working>../Cleopatra/Transfer

== How to change the kinematic E-Z line? ==

see [[#How to simulate the kinematics?]]

The E-Z lines are stored in fxList in transfer.root

In Monitors.C, at the end or Monitors::Terminate().

you can see the fxList.

== How to simulate the kinematics? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|}

edit
* reactionConfig.txt 
* detectorGeo.txt 
* Ex.txt 

Then run
working>../Cleopatra/Transfer

after that, 2 files will be generated, 1) reaction.dat, 2) transfer.root

a tree is inside transfer.root.

you can see the tree branches by

root> tree->Print()

I hope the branch name is self-explained.

In Armory, there is a root macro Check_Transfer.C

working>root '../Armory/Check_Transfer.C("transfer.root")'

The macro load the transfer.root and plot the e-z plot, the recoil, recoil radius vs thetaCM etc...

== How to do DWBA calculation ? ==

{| class="wikitable"
|-
|CAUTION: If the code is git clone or download recently, please go to ~/digios/analysis/Cleopatra, and
Cleopatra>make
|-
|CAUTION: ONLY IN LINUX, because Ptolemy only work in Linux.
|}

edit the file DWBA, then

working>./Cleopatra example 1 1 1 1 0 [minAng] [maxAng] [angStep]

This will generate the example.in, feed to Ptolemy, output example.out, extract the differential cross section into

* example.Xsec.txt
* example.root

And plot the d.s.c. using example.root

It will also generate example.Ex.txt

For arguments meaning, use Cleopatra without any argument

working>./Cleopatra

== How to do kinematics simulation with DWBA differential cross section ? ==

see [[#How to do DWBA calculation ?]] first.

edit
* reactionConfig.txt 
* detectorGeo.txt 
* example 

Make sure the reaction in the reactionConfig.txt is matching with that in example

working>./Cleopatra example 1 1 1 0 1 0 180 1

The excitation levels is using example.Ex.txt.

The bash script will calculate the DWBA d.s.c. using Cleopatra, then using ../Cleopatra/Transfer to do the simulation.

see [[#How to simulate the kinematics?]]

= How to do trace analysis ? =

updated Feb-12, 2021

simply

working>Process_RUN [RunNum] 1 -2 [number_of_worker] [Option_for_Monitors]

Updated Nov-6, 2019
The GEBSort_nogeb_trace was generated, Simple run ./process_run with option is fine

--------------------------------
First, the GEBSort code has to be recompile by changing the file digios/GEBSort/bin_rcnp.C

in that file, comment out the trace (line ?)

Then, recompile

GEBSort>make offline

Now the gen_runXXX.root will contains trace data.

go back to working directory

working>./process_run [RUNNUM] 1 1 2 1

The 4th argument is 2, that means the GeneralSort (or the mapping ) will use ../Amrory/GeneralSortTrace.C instead of ../Amory/GeneralSort.C

The 4th argument can be also be more than 2, say, when it is N, it means it will use Proof, a parallel computing framework built-in in root that use N cores.

To display the trace, we can use ../Armory/readTrace.C ( this macro is kind of shitty.....)

= How to count a 1D histogram for a given range ? =

After ./process_run, a function Check1D() is loaded.

= How to fit the excitation spectrum ? =

If the reaction.dat is set properly, after ./process_run, the excite() function will give you the excitation spectrum.

root>excite()

You can use the fitAuto() function to auto fit the spectrum by

root>fitAuto(hEx)

For more option

fitAuto( [hist name], [BG estimation] )

-------------------------------
Or you can can fit N-Gauss + 1 linear function. In this case, edit the AutFit_para.txt

root>fitNGaussP1(hEx)