Amsterdam Density Functional Modeling Suite: Difference between revisions

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Revision as of 15:32, 8 May 2019

Introduction[edit]

The ADF (Amsterdam Density Functional) Modeling Suite offers powerful computational chemistry tools for many research areas such as homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry.

Users have access to the products in the ADF Modeling Suite: ADF, ADF-GUI, BAND, BAND-GUI, DFTB, ReaxFF, COSMO-RS, QE-GUI, and NBO6.

ADF on Graham[edit]

ADF 2017.207 and 2016.106 are installed on the new cluster Graham with modules. Free access for users on Graham.

Version selection[edit]

User can chose which version of ADF to use, 2016.106 or 2017.207 

#for ADF 2017.207
module load adf/2017.207

#for ADF 2016.106
module load adf/2016.106

Job Submission[edit]

Graham uses your ComputeCanada(CC) user account, not your Sharcnet account anymore. Each research group has a default account with your supervisor's userid (PI'sid) named def-PI'sid (type 'groups' on Graham will show the groups you are in).

If this is your first time to use Graham, you can add the following line to your .bash_profile file 

export SLURM_ACCOUNT=def-PI'id
export SBATCH_ACCOUNT=$SLURM_ACCOUNT 
export SALLOC_ACCOUNT=$SLURM_ACCOUNT

Otherwise, you will have to include #SBATCH_ACCOUNT=def-PI'sid in submit script for each job.

Here is an example for a full-node ADF job named adf_test.sh: 

#!/bin/bash
#SBATCH --nodes=1 --ntasks-per-node=32  # 1 node with 32 cpus, you can modify it
#SBATCH --mem-per-cpu=2G                # memory, should be <4G for full node job
#SBATCH --time=00-03:00                 # time (DD-HH:MM)
#SBATCH --output=adf_test.log          # output .log file
module load adf/2017.207
ADF adf_test.inp                # ADF command

If the job needs more mem-per-cpu, then the job has to use multi-nodes, for example: 

#SBATCH --nodes=4 --ntasks-per-node=8  # 4 nodes with 32 cpus, 8 cpus per node
#SBATCH --mem-per-cpu=6G              # 6G memory per cpu

adf_test.inp is an example input file for one-step ADF calculation 

 Title WATER Geometry Optimization with Delocalized Coordinates

 Atoms
    O             0.000000     0.000000     0.000000
    H             0.000000    -0.689440    -0.578509
    H             0.000000     0.689440    -0.578509
 End

 Basis
 Type TZP
 Core Small
 End

 Geometry
  Optim Deloc
  Converge 0.0000001
 End

 End Input

Change file permission for adf_test.sh to be executable, i.e., 

chmod 750 adf_test.sh

Submit the job using sbatch 

sbatch adf_sbatch.sh

Chechk for job status 

squeue -u userid  #check your own jobs in the queue
or 
sacct   #your job history

The same as on other Sharcnet clusters, the runtime files are under /scratch/userid/jobid/

Examples[edit]

Example for adf_test can be found on Graham under 

/home/jemmyhu/tests/test_ADF/2017.207/test_adf/

Some user may do multi-step ADF runs within one job, see GO_H2O.run and GO_H2O.sh example under 

/home/jemmyhu/tests/test_ADF/2017.207/test_adf/

The same procedure applies to BAND job, see band_test.inp and band_test.sh examples under 

/home/jemmyhu/tests/test_ADF/2017.207/test_band

Run ADF-GUI on Graham's vdi node using VNC[edit]

ssh x11 rendering is very slow for remote GUI application such as ADF-GUI. User should use VNC to connect to graham and run ADF-GUI on Graham.

Example for how to install, connect and run ADF-GUI using TigerVNC has been given in TigerVNC-for-ADF-GUI

ADF on other Sharcnet clusters (no change at this point)[edit]

ADF 2016.106, 2014.05 and 2013.01 are available on several clusters
To use ADF, you need to add a module load line in your .bash_profile configuration file 

module load adf/version

for example to use ADF-2014.05, the module load line will be 

module load adf/2014.05

logout, then login again to effect the setting (this license setting is temporary before we get a full renewed license) .

To verify which ADF version and PATH, type 'which adf', it will return something like 

/opt/sharcnet/adf/version/bin/adf

Example Job[edit]

  • Example 1: Here is an example for GO_H2O-adf.inp
Title WATER Geometry Optimization with Delocalized Coordinates

Atoms
    O             0.000000     0.000000     0.000000
    H             0.000000    -0.689440    -0.578509
    H             0.000000     0.689440    -0.578509
End

Basis
 Type TZP
 Core Small
End

Geometry
  Optim Deloc
  Converge 0.0000001
End

End Input

Example for GO_H2O-adf.inp and the run results can be found in 

/home/jemmyhu/tests/test_ADF/orca/test_2014.05
  • Example 2: input for multiple steps, NMR_B3LYP.run
#!/bin/sh

$ADFBIN/adf << eor
title PF3-NMR-B3LYP

basis
 type DZP
 core None
end

Define
  RPF  =   1.641314
  AXPF = 119.702107
End

Atoms
P       0.00000000       0.00000000       1.00000000
F      -0.71283358       1.23466398       1.81325568
F      -0.71283358      -1.23466398       1.81325568
F       1.42566716       0.00000000       1.81325568
End

integration 6.0

noprint sfo

xc
 hybrid B3LYP
end

save TAPE10

end input
eor
rm logfile

$ADFBIN/nmr << eor
NMR
  U1K  BEST
  Out  TENS
  Nuc  1  2
  SCF 1.d-4
End
eor

mv TAPE21 PF3_1.t21
rm TAPE15 TAPE10
rm logfile

$ADFBIN/adf << eor
title PF3-NMR-B3LYP ZORA SCALAR

basis
 type DZP
 core None
end

Define
  RPF  =   1.641314
  AXPF = 119.702107
End

Atoms
P       0.00000000       0.00000000       1.00000000
F      -0.71283358       1.23466398       1.81325568
F      -0.71283358      -1.23466398       1.81325568
F       1.42566716       0.00000000       1.81325568
End

integration 6.0

noprint sfo

xc
 hybrid B3LYP
end

RELATIVISTIC SCALAR ZORA

save TAPE10

end input
eor
rm logfile

$ADFBIN/nmr << eor
NMR
  U1K  BEST
  Out  TENS
  Nuc  1  2
  SCF 1.d-4
End
eor

mv TAPE21 PF3_2.t21
rm TAPE15 TAPE10
rm logfile

$ADFBIN/adf << eor
title PF3-NMR-B3LYP ZORA SPINORBIT

basis
 type DZP
 core None
end

Define
  RPF  =   1.641314
  AXPF = 119.702107
End

Atoms Z-mat
  1  Xx 0  0  0
  2  P  1  0  0   1.0
  3  F  2  1  0   RPF   AXPF
  4  F  2  1  3   RPF   AXPF   120.
  5  F  2  1  3   RPF   AXPF  -120.
End

symmetry nosym

integration 6.0

noprint sfo

xc
 hybrid B3LYP
end

RELATIVISTIC SPINORBIT ZORA

save TAPE10

end input
eor
rm logfile

$ADFBIN/nmr << eor
ZSOAO2007

NMR
  U1K  BEST
  Out  TENS
  Nuc  1  2
  SCF 1.d-4
End
eor

Example for NMR_B3LYP.run and the run results can be found in 

/home/jemmyhu/tests/test_ADF/saw/NMR_B3LYP

You can also find many examples in /opt/sharcnet/adf/2016.106/examples/

General Notes[edit]

  • ADF GUI on Viz workstations, user needs a Sharcnet account to login to one of the viz workstations
    • To run adfview on ati (non-nvidia) viz machines viz10-uwo, viz11-uwo and vdi-centos6.user.sharcnet.ca over vnc (remote desktop blue icon on systems page) one should first run LD_PRELOAD=adfview
    • To run GUI applications, you need to turn on a X-Windows (Xming, etc) on your PC before login to a SHARCNET system.
    • ADF GUI applications (adfjobs, adfinput, adfview, bandinput, etc) can be run on the Vidualization workstations, or on the development nodes (orc-dev1, ..., orc-dev4) on orca, e.g., login to orca, then ssh to a dev node, e.g. ssh to orc-dev4 with X-Window enabled as
ssh -Y orc-dev4
  • ADF mpi job size
    • Depending on your molecule size (data size), ADF/BAND can scale well via MPI up to a 32 cpu job. Normally, please run 8- or 16- way ADF MPI jobs for medium-sized molecules. We do not recommend to run more than 32-way ADF mpi jobs on SHARCNET clusters.

References[edit]

o Documentation ADF 2012
http://www.scm.com/Doc/Doc2012/

Message Passing Interface

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