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Commit 0a23a308 authored by dmar's avatar dmar
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add folder for the 6th exercise

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Exercises/Exercise-6/PBE_ethanol.inp 0 → 100644
View file @ 0a23a308
&GLOBAL
PROJECT output_PBE_ethanol
RUN_TYPE GEO_OPT
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&GEO_OPT
OPTIMIZER BFGS
MAX_ITER 200
MAX_DR 0.001
RMS_DR 0.0003
MAX_FORCE 0.0001
RMS_FORCE 0.00003
&BFGS
USE_MODEL_HESSIAN yes
&END BFGS
&END GEO_OPT
&PRINT
&TRAJECTORY on
FORMAT xyz
&EACH
GEO_OPT 1
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&PRINT
&MO_CUBES
ADD_LAST SYMBOLIC
NHOMO 5
NLUMO 5
&END MO_CUBES
&END PRINT
&MGRID
CUTOFF 400
&END MGRID
CHARGE 0
&POISSON
PERIODIC NONE
PSOLVER WAVELET
&END POISSON
&QS
METHOD GAPW ! use gaussians and plane waves
&END QS
&SCF
&OT
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
N_DIIS 7
&END
SCF_GUESS RESTART
EPS_SCF 5.0E-6
MAX_SCF 50
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 500
&END
&END SCF
&XC
&XC_FUNCTIONAL PBE ! second order of DFT
&END XC_FUNCTIONAL
&END XC
&END DFT
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&PROGRAM_RUN_INFO
&EACH
GEO_OPT 1
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
PERIODIC NONE
ABC 10 10 10
&END CELL
&COORD
O -1.147741 -0.406185 0.000000
C -0.083071 0.548036 0.000000
C 1.225516 -0.215926 0.000000
H -1.993992 0.055874 0.000000
H -0.148310 1.193128 0.887383
H -0.148310 1.193128 -0.887383
H 2.074218 0.474339 0.000000
H 1.299343 -0.852891 0.884848
H 1.299343 -0.852891 -0.884848
&END COORD
&TOPOLOGY
&CENTER_COORDINATES
&END
&END TOPOLOGY
&KIND H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
Exercises/Exercise-6/PBE_ethene.inp 0 → 100644
View file @ 0a23a308
&GLOBAL
PROJECT output_PBE_ethene
RUN_TYPE GEO_OPT
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&GEO_OPT
OPTIMIZER BFGS
MAX_ITER 200
MAX_DR 0.001
RMS_DR 0.0003
MAX_FORCE 0.0001
RMS_FORCE 0.00003
&BFGS
USE_MODEL_HESSIAN yes
&END BFGS
&END GEO_OPT
&PRINT
&TRAJECTORY on
FORMAT xyz
&EACH
GEO_OPT 1
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&PRINT
&MO_CUBES
ADD_LAST SYMBOLIC
NHOMO 5
NLUMO 5
&END MO_CUBES
&END PRINT
&MGRID
CUTOFF 400
&END MGRID
CHARGE 0
&POISSON
PERIODIC NONE
PSOLVER WAVELET
&END POISSON
&QS
METHOD GAPW !use gaussians and plane waves
&END QS
&SCF
&OT
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
N_DIIS 7
&END
SCF_GUESS RESTART
EPS_SCF 5.0E-6
MAX_SCF 50
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 500
&END
&END SCF
&XC
&XC_FUNCTIONAL PBE !second order of DFT
&END XC_FUNCTIONAL
&END XC
&END DFT
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&PROGRAM_RUN_INFO
&EACH
GEO_OPT 1
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
PERIODIC NONE
ABC 10 10 10
&END CELL
&COORD
H 2.5558925119 4.9201502245 3.9999999733
H 2.5617214834 3.0599837703 4.0000000267
C 3.3235178526 3.9916405319 4.0000000002
C 4.6493228423 3.9951429630 3.9999999995
H 5.4118318595 4.9261779106 4.0000000269
H 5.4167134504 3.0669045998 3.9999999735
&END COORD
&TOPOLOGY
&CENTER_COORDINATES
&END
&END TOPOLOGY
&KIND H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
Exercises/Exercise-6/PBE_h2o.inp 0 → 100644
View file @ 0a23a308
&GLOBAL
PROJECT output_PBE_h2o
RUN_TYPE GEO_OPT
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&GEO_OPT
OPTIMIZER BFGS
MAX_ITER 200
MAX_DR 0.001
RMS_DR 0.0003
MAX_FORCE 0.0001
RMS_FORCE 0.00003
&BFGS
USE_MODEL_HESSIAN yes
&END BFGS
&END GEO_OPT
&PRINT
&TRAJECTORY on
FORMAT xyz
&EACH
GEO_OPT 1
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&PRINT
&MO_CUBES
ADD_LAST SYMBOLIC
NHOMO 5
NLUMO 5
&END MO_CUBES
&END PRINT
&MGRID
CUTOFF 400
&END MGRID
CHARGE 0
&POISSON
PERIODIC NONE
PSOLVER WAVELET
&END POISSON
&QS
METHOD GAPW !use gaussians and plane waves
&END QS
&SCF
&OT
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
N_DIIS 7
&END
SCF_GUESS RESTART
EPS_SCF 5.0E-6
MAX_SCF 50
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 500
&END
&END SCF
&XC
&XC_FUNCTIONAL PBE !second order of DFT
&END XC_FUNCTIONAL
&END XC
&END DFT
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&PROGRAM_RUN_INFO
&EACH
GEO_OPT 1
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
PERIODIC NONE
ABC 10 10 10
&END CELL
&COORD
H 2.5558925119 3.0 4.
O 4.00 3.5 4.
H 5.4167134504 3.0669045998 4.
&END COORD
&TOPOLOGY
&CENTER_COORDINATES
&END
&END TOPOLOGY
&KIND H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
Exercises/Exercise-6/PBE_ts.inp 0 → 100644
View file @ 0a23a308
&GLOBAL
PROJECT output_PBE_ts
RUN_TYPE ENERGY
PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&PRINT
&MO_CUBES
ADD_LAST SYMBOLIC
NHOMO 5
NLUMO 5
&END MO_CUBES
&END PRINT
&MGRID
CUTOFF 400
&END MGRID
CHARGE 0
&POISSON
PERIODIC NONE
PSOLVER WAVELET
&END POISSON
&QS
METHOD GAPW !use gaussians and plane waves
&END QS
&SCF
&OT
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
N_DIIS 7
&END
SCF_GUESS RESTART
EPS_SCF 5.0E-6
MAX_SCF 50
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 500
&END
&END SCF
&XC
&XC_FUNCTIONAL PBE !second order of DFT
&END XC_FUNCTIONAL
&END XC
&END DFT
&PRINT
&FORCES off
&END FORCES
&GRID_INFORMATION
&END GRID_INFORMATION
&PROGRAM_RUN_INFO
&EACH
GEO_OPT 1
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
PERIODIC NONE
ABC 15 15 15
&END CELL
&COORD
O 8.9032129608 9.3745830914 9.0525205546
C 9.8609284027 10.6759920837 10.0457624100
C 11.0319812276 9.8807945923 10.1470867497
H 8.2336288866 8.9324129403 9.6176159689
H 9.1771724615 10.7851705894 10.8901323339
H 9.7764660070 11.4567788980 9.2891902695
H 11.8812807399 10.1162358264 9.5057571154
H 11.2640746621 9.4127130317 11.1041995985
H 10.0937061517 9.0932694467 9.4453939995
&END COORD
&TOPOLOGY
&CENTER_COORDINATES
&END
&END TOPOLOGY
&KIND H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
Exercises/Exercise-6/run_ethanol 0 → 100644
View file @ 0a23a308
#!/bin/bash -l
#
# CP2K on Piz Daint: 64 nodes, 1 MPI task per node, 12 OpenMP threads per task
#
#SBATCH --job-name=ethanol
#SBATCH --time=00:30:00
#SBATCH --nodes=1
#SBATCH --partition=debug
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --constraint=gpu
#========================================
# load modules and run simulation
module load daint-gpu
module load CP2K
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
ulimit -s unlimited
srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c $SLURM_CPUS_PER_TASK cp2k.psmp -i PBE_ethanol.inp -o PBE_ethanol.out
Exercises/Exercise-6/run_ethene 0 → 100644
View file @ 0a23a308
#!/bin/bash -l
#
# CP2K on Piz Daint: 64 nodes, 1 MPI task per node, 12 OpenMP threads per task
#
#SBATCH --job-name=ethene
#SBATCH --time=00:30:00
#SBATCH --nodes=1
#SBATCH --partition=debug
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --constraint=gpu
#========================================
# load modules and run simulation
module load daint-gpu
module load CP2K
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
ulimit -s unlimited
srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c $SLURM_CPUS_PER_TASK cp2k.psmp -i PBE_ethene.inp -o PBE_ethene.out
Exercises/Exercise-6/run_h2o 0 → 100644
View file @ 0a23a308
#!/bin/bash -l
#
# CP2K on Piz Daint: 64 nodes, 1 MPI task per node, 12 OpenMP threads per task
#
#SBATCH --job-name=h2o
#SBATCH --time=00:30:00
#SBATCH --nodes=1
#SBATCH --partition=debug
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --constraint=gpu
#========================================
# load modules and run simulation
module load daint-gpu
module load CP2K
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
ulimit -s unlimited
srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c $SLURM_CPUS_PER_TASK cp2k.psmp -i PBE_h2o.inp -o PBE_h2o.out
Exercises/Exercise-6/run_ts 0 → 100644
View file @ 0a23a308
#!/bin/bash -l
#
# CP2K on Piz Daint: 64 nodes, 1 MPI task per node, 12 OpenMP threads per task
#
#SBATCH --job-name=ts
#SBATCH --time=00:30:00
#SBATCH --nodes=1
#SBATCH --partition=debug
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --constraint=gpu
#========================================
# load modules and run simulation
module load daint-gpu
module load CP2K
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
ulimit -s unlimited
srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c $SLURM_CPUS_PER_TASK cp2k.psmp -i PBE_ts.inp -o PBE_ts.out
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