Orca update

docs.it4i/software/orca.md

@@ -2,65 +2,132 @@
 
 ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
 
-## Making ORCA Available
+## ORCA Available on the Cluster
 
-The following module command makes the latest version of orca available to your session
+Many versions of ORCA is available on our clusters. You can list all versions by `ml av` command.
 
 ```console
-$ module load ORCA/3_0_3-linux_x86-64
+$ ml av orca
+-------------------------- /apps/modules/chem --------------------------
+  ORCA/4_0_0-linux_x86-64    ORCA/4_0_1-linux_x86-64    ORCA/4.0.1.2 (D)
+
+  Where:
+   D:  Default Module
+```
+
+## Serial Computation With ORCA
+
+You can test serial computation with this simple input file. Create a file called orca_serial.inp and fill it with following ORCA commands.
+
+```bash
+    # Taken from the Orca manual
+    # https://orcaforum.cec.mpg.de/OrcaManual.pdf
+    ! HF SVP
+    * xyz 0 1
+      C 0 0 0
+      O 0 0 1.13
+    *
+```
+
+Next, create a PBS submission file (interactive job can be used too).
+
+```bash
+#!/bin/bash
+#PBS -S /bin/bash
+#PBS -N ORCA_SERIAL
+#PBS -l select=1
+#PBS -q qexp
+
+ml ORCA/4.0.1.2
+${EBROOTORCA}orca orca_serial.inp
 ```
 
-### Dependency
+Submit the job to the queue and wait before it ends. Then you can find an output log in your working directory.
 
 ```console
-$ module list
-Currently Loaded Modulefiles:
-  1) /opt/modules/modulefiles/oscar-modules/1.0.3(default)
-  2) GCC/4.9.3-binutils-2.25
-  3) binutils/2.25-GCC-4.9.3-binutils-2.25
-  4) GNU/4.9.3-2.25
-  5) icc/2015.3.187-GNU-4.9.3-2.25
-  6) ifort/2015.3.187-GNU-4.9.3-2.25
-  7) iccifort/2015.3.187-GNU-4.9.3-2.25
-  8) numactl/2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25
-  9) hwloc/1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25
-  10) OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25
-  11) ORCA/3_0_3-linux_x86-64
+$ qsub submit_serial.pbs
+1417552.dm2
+
+$ ll ORCA_SERIAL.*
+-rw------- 1 hra0031 hra0031     0 Aug 21 12:24 ORCA_SERIAL.e1417552
+-rw------- 1 hra0031 hra0031 20715 Aug 21 12:25 ORCA_SERIAL.o1417552
+
+$ cat ORCA_SERIAL.o1417552
+
+                                 *****************
+                                 * O   R   C   A *
+                                 *****************
+
+           --- An Ab Initio, DFT and Semiempirical electronic structure package ---
+
+                  #######################################################
+                  #                        -***-                        #
+                  #  Department of molecular theory and spectroscopy    #
+                  #              Directorship: Frank Neese              #
+                  # Max Planck Institute for Chemical Energy Conversion #
+                  #                  D-45470 Muelheim/Ruhr              #
+                  #                       Germany                       #
+                  #                                                     #
+                  #                  All rights reserved                #
+                  #                        -***-                        #
+                  #######################################################
+
+
+                         Program Version 4.0.1.2 - RELEASE -
+
+...
+
+                             ****ORCA TERMINATED NORMALLY****
+TOTAL RUN TIME: 0 days 0 hours 0 minutes 1 seconds 47 msec
 ```
 
-## Example Single Core Job
+## Running ORCA in Parallel
 
-Create a file called orca_serial.inp that contains the following orca commands
+Your serial computation can be converted to parallel in a very simple way. You simply have to specify the number of parallel processes by directive **%pal**. In this example, 4 nodes, 16 cores each are used.
 
-```cpp
-    # My first ORCA calculation :-)
-    #
+!!! warning
+    Don't use **! PAL** directive as only PAL2 to PAL8 is recognized!
+
+```bash
     # Taken from the Orca manual
     # https://orcaforum.cec.mpg.de/OrcaManual.pdf
     ! HF SVP
+    %pal
+      nprocs 64 # 4 nodes, 16 cores each
+    end
     * xyz 0 1
       C 0 0 0
       O 0 0 1.13
     *
 ```
 
-Create a Sun Grid Engine submission file called submit_serial.sh that looks like this
+You also need to edit the previously used PBS submission file. You have to specify number of nodes, cores and MPI-processes to run.
 
-```console
-!/bin/bash
+```bash
+#!/bin/bash
+#PBS -S /bin/bash
+#PBS -N ORCA_PARALLEL
+#PBS -l select=4:ncpus=16:mpiprocs=16
+#PBS -q qexp
 
-module load ORCA/3_0_3-linux_x86-64
-orca orca_serial.inp
+ml ORCA/4.0.1.2
+${EBROOTORCA}/orca orca_parallel.inp
 ```
 
-Submit the job to the queue with the command
+!!! note 
+    When running ORCA in parallel, ORCA should **NOT** be started with mpirun: e.g. mpirun -np 4 orca etc. like many MPI programs and has to be called with full pathname.
+
+Submit this job to the queue and see the output file.
 
 ```console
-$ qsub -q qexp -I -l select=1
-qsub: waiting for job 196821.isrv5 to start
-qsub: job 196821.isrv5 ready
-[username@r37u04n944 ~]$ ./submit_serial.sh
+$ qsub submit_parallel.pbs
+1417598.dm2
 
+$ ll ORCA_PARALLEL.*
+-rw-------  1 hra0031 hra0031     0 Aug 21 13:12 ORCA_PARALLEL.e1417598
+-rw-------  1 hra0031 hra0031 23561 Aug 21 13:13 ORCA_PARALLEL.o1417598
+
+$ cat ORCA_PARALLEL.o1417598
 
                                  *****************
                                  * O   R   C   A *
@@ -80,19 +147,44 @@ qsub: job 196821.isrv5 ready
                   #                        -***-                        #
                   #######################################################
 
+
+                         Program Version 4.0.1.2 - RELEASE -
 ...
 
-                             ****ORCA TERMINATED NORMALLY****
-TOTAL RUN TIME: 0 days 0 hours 0 minutes 2 seconds 796 msec
-[username@r37u04n944 orca]$ logout
+           ************************************************************
+           *        Program running with 64 parallel MPI-processes    *
+           *              working on a common directory               *
+           ************************************************************
 
-qsub: job 196821.isrv5 completed
+...
+                             ****ORCA TERMINATED NORMALLY****
+TOTAL RUN TIME: 0 days 0 hours 0 minutes 11 seconds 859 msec
 ```
 
+You can see, that the program was running with 64 parallel MPI-processes. In version 4.0.1.2, only the following modules are parallelized:
+
+* ANOINT
+* CASSCF / NEVPT2
+* CIPSI
+* CIS/TDDFT
+* CPSCF
+* EPRNMR
+* GTOINT
+* MDCI (Canonical-, PNO-, DLPNO-Methods)
+* MP2 and RI-MP2 (including Gradient and Hessian)
+* MRCI
+* PC
+* ROCIS
+* SCF
+* SCFGRAD
+* SCFHESS
+* SOC
+* Numerical Gradients and Frequencies
+
 ## Register as a User
 
-You are encouraged to register as a user of Orca at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
+You are encouraged to register as a user of ORCA at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
 
 ## Documentation
 
-A comprehensive [.pdf](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.
+A comprehensive [PDF](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.