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New page: The VASP-MGCM (Vasp-Multigrid Continuum Model) was compiled in the VASP 5.3.3 version (normal and gamma version). To perform a calculation of a solvated system PLEASE read first the attach... |
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=WARNING: THIS PAGE IS DEPRECATED. PLEASE GO HERE:= | |||
[[VASP-MGCM (solvation_module)]] | |||
---- | The VASP-MGCM (Vasp-Multigrid Continuum Model) available in tekla2 has been compiled in the VASP 5.3.3 version (normal and gamma version). To perform a calculation of a solvated system PLEASE read first the following pdf guide --> [http://aliga.iciq.es/wiki/index.php/Image:vasp_mgcm_guide.pdf vasp_mgcm_guide.pdf]. After that, the user needs to slightly modify the VASP running script. The two only lines that have to be changed are those corresponding to the module and executable calls. For some reason (most likely due to the different fortran libraries available in the tekla2 queues) the code runs at a reasonable computational cost in the c8m24.q. If there is enough space in this queue run your calculation there, otherwise use the c24m128ib.q although the speed is much lower there at this moment. | ||
- Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (normal version): | |||
-------------------------------------------------------------------------------------------- | |||
mpirun -np $NSLOTS vasp_mgcm | #!/bin/bash | ||
# - Dr. Nuria Lopez Group - | |||
########################################## | |||
# SGE Parameters | |||
########################################## | |||
#$ -S /bin/bash | |||
#$ -N example1 | |||
#$ -cwd | |||
#$ -masterq c8m24.q | |||
#$ -pe c8m24_mpi 8 | |||
#$ -m ae | |||
#$ -o o_$JOB_NAME.$JOB_ID | |||
#$ -e e_$JOB_NAME.$JOB_ID | |||
########################################## | |||
# Load Evironment Variables | |||
########################################## | |||
. /etc/profile.d/modules.sh | |||
module load vasp/5.3.3-mgarciar | |||
########################################## | |||
# Running Job | |||
########################################## | |||
export OMP_NUM_THREADS=1 | |||
echo $PWD >> o_$JOB_NAME.$JOB_ID | |||
echo $TMP >> o_$JOB_NAME.$JOB_ID | |||
mpirun -np $NSLOTS vasp_mgcm | |||
-------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | ||
Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (gamma-version): | - Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (gamma-version): | ||
-------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | ||
#!/bin/bash | #!/bin/bash | ||
# - Dr. Nuria Lopez Group - | # - Dr. Nuria Lopez Group - | ||
########################################## | ########################################## | ||
# SGE Parameters | # SGE Parameters | ||
########################################## | ########################################## | ||
#$ -S /bin/bash | #$ -S /bin/bash | ||
#$ -N example2 | #$ -N example2 | ||
#$ -cwd | #$ -cwd | ||
#$ -masterq c8m24.q | #$ -masterq c8m24.q | ||
#$ -pe c8m24_mpi 8 | #$ -pe c8m24_mpi 8 | ||
#$ -m ae | #$ -m ae | ||
#$ -o o_$JOB_NAME.$JOB_ID | #$ -o o_$JOB_NAME.$JOB_ID | ||
#$ -e e_$JOB_NAME.$JOB_ID | #$ -e e_$JOB_NAME.$JOB_ID | ||
########################################## | ########################################## | ||
# Load Evironment Variables | # Load Evironment Variables | ||
########################################## | ########################################## | ||
. /etc/profile.d/modules.sh | . /etc/profile.d/modules.sh | ||
module load vasp/5.3.3-mgarciar-GAMMA | module load vasp/5.3.3-mgarciar-GAMMA | ||
########################################## | ########################################## | ||
# Running Job | # Running Job | ||
########################################## | ########################################## | ||
export OMP_NUM_THREADS=1 | export OMP_NUM_THREADS=1 | ||
echo $PWD >> o_$JOB_NAME.$JOB_ID | |||
echo $TMP >> o_$JOB_NAME.$JOB_ID | |||
mpirun -np $NSLOTS vasp_mgcm | |||
-------------------------------------------------------------------------------------------- | |||
For further details about the VASP-MGCM please read: J. Chem. Theory Comput., 2016, 12 (3), pp 1331–1341. If one has further questions send an e-mail to Dr. Miquel Garcia-Ratés (ask Nuria Vendrell for the e-mail address). | |||
Latest revision as of 17:37, 6 February 2020
WARNING: THIS PAGE IS DEPRECATED. PLEASE GO HERE:[edit]
The VASP-MGCM (Vasp-Multigrid Continuum Model) available in tekla2 has been compiled in the VASP 5.3.3 version (normal and gamma version). To perform a calculation of a solvated system PLEASE read first the following pdf guide --> vasp_mgcm_guide.pdf. After that, the user needs to slightly modify the VASP running script. The two only lines that have to be changed are those corresponding to the module and executable calls. For some reason (most likely due to the different fortran libraries available in the tekla2 queues) the code runs at a reasonable computational cost in the c8m24.q. If there is enough space in this queue run your calculation there, otherwise use the c24m128ib.q although the speed is much lower there at this moment.
- Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (normal version):
#!/bin/bash # - Dr. Nuria Lopez Group - ########################################## # SGE Parameters ########################################## #$ -S /bin/bash #$ -N example1 #$ -cwd #$ -masterq c8m24.q #$ -pe c8m24_mpi 8 #$ -m ae #$ -o o_$JOB_NAME.$JOB_ID #$ -e e_$JOB_NAME.$JOB_ID ########################################## # Load Evironment Variables ########################################## . /etc/profile.d/modules.sh module load vasp/5.3.3-mgarciar ########################################## # Running Job ########################################## export OMP_NUM_THREADS=1 echo $PWD >> o_$JOB_NAME.$JOB_ID echo $TMP >> o_$JOB_NAME.$JOB_ID mpirun -np $NSLOTS vasp_mgcm
- Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (gamma-version):
#!/bin/bash # - Dr. Nuria Lopez Group - ########################################## # SGE Parameters ########################################## #$ -S /bin/bash #$ -N example2 #$ -cwd #$ -masterq c8m24.q #$ -pe c8m24_mpi 8 #$ -m ae #$ -o o_$JOB_NAME.$JOB_ID #$ -e e_$JOB_NAME.$JOB_ID ########################################## # Load Evironment Variables ########################################## . /etc/profile.d/modules.sh module load vasp/5.3.3-mgarciar-GAMMA ########################################## # Running Job ########################################## export OMP_NUM_THREADS=1 echo $PWD >> o_$JOB_NAME.$JOB_ID echo $TMP >> o_$JOB_NAME.$JOB_ID mpirun -np $NSLOTS vasp_mgcm
For further details about the VASP-MGCM please read: J. Chem. Theory Comput., 2016, 12 (3), pp 1331–1341. If one has further questions send an e-mail to Dr. Miquel Garcia-Ratés (ask Nuria Vendrell for the e-mail address).