Add Diels-Alder example

arcann-chem · Oct 3, 2024 · 79d0778 · 79d0778
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diff --git a/examples/diels_alder_ethene_13butadiene/R/000-training/input.json b/examples/diels_alder_ethene_13butadiene/R/000-training/input.json
@@ -0,0 +1,5 @@
+{
+    "user_machine_keyword_train": "a100_hpc1",
+    "user_machine_keyword_freeze": "v100_hpc1",
+    "user_machine_keyword_compress": "v100_hpc1"
+}
diff --git a/examples/diels_alder_ethene_13butadiene/R/000-training/used_input.json b/examples/diels_alder_ethene_13butadiene/R/000-training/used_input.json
@@ -0,0 +1,18 @@
+{
+    "user_machine_keyword_train": "a100_hpc1",
+    "user_machine_keyword_freeze": "v100_hpc1",
+    "user_machine_keyword_compress": "v100_hpc1",
+    "job_email": "",
+    "use_initial_datasets": true,
+    "use_extra_datasets": false,
+    "deepmd_model_version": 2.1,
+    "job_walltime_train_h": 12.0,
+    "mean_s_per_step": 0.108,
+    "start_lr": 0.001,
+    "stop_lr": 1e-06,
+    "decay_rate": 0.9172759353897796,
+    "decay_steps": 5000,
+    "decay_steps_fixed": false,
+    "numb_steps": 400000,
+    "numb_test": 0
+}
diff --git a/examples/diels_alder_ethene_13butadiene/R/001-exploration/input.json b/examples/diels_alder_ethene_13butadiene/R/001-exploration/input.json
@@ -0,0 +1,9 @@
+{
+    "user_machine_keyword_exp": "v100_nvs",
+    "atomsk_path": "/lustre/fsn1/worksf/projects/rech/kro/commun/programs/atomsk/0.13.1/atomsk",
+    "timestep_ps": 0.00025,
+    "previous_start": false,
+    "print_interval_mult": 0.0005,
+    "ignore_first_x_ps": 0.1,
+    "sigma_low": 0.15
+}
diff --git a/examples/diels_alder_ethene_13butadiene/R/001-exploration/used_input.json b/examples/diels_alder_ethene_13butadiene/R/001-exploration/used_input.json
@@ -0,0 +1,25 @@
+{
+    "user_machine_keyword_exp": "v100_nvs",
+    "job_email": "",
+    "atomsk_path": "/home/rdavid/programs/apps/atomsk/0.13.1/atomsk",
+    "vmd_path": "/home/sw/target/generic/app/vmd/vmd-1.9.4a55/bin/vmd",
+    "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps"],
+    "traj_count": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
+    "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0],
+    "timestep_ps": [0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025],
+    "previous_start": [false, false, false, false, false, false, false, false, false, false],
+    "disturbed_start": [false, false, false, false, false, false, false, false, false, false],
+    "print_interval_mult": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005],
+    "job_walltime_h": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
+    "exp_time_ps": [10.0, 10.0, 10.0, 10.0, 20.0, 10.0, 10.0, 10.0, 10.0, 20.0],
+    "max_exp_time_ps": [400, 400, 400, 400, 400, 400, 400, 400, 400, 400],
+    "max_candidates": [50, 50, 50, 50, 50, 50, 50, 50, 50, 50],
+    "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15],
+    "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7],
+    "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
+    "ignore_first_x_ps": [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1],
+    "disturbed_start_value": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+    "disturbed_start_indexes": [[], [], [], [], [], [], [], [], [], []],
+    "disturbed_candidate_value": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+    "disturbed_candidate_indexes": [[], [], [], [], [], [], [], [], [], []]
+}
diff --git a/examples/diels_alder_ethene_13butadiene/R/001-labeling/used_input.json b/examples/diels_alder_ethene_13butadiene/R/001-labeling/used_input.json
@@ -0,0 +1,10 @@
+{
+    "user_machine_keyword_label": "cpu_hpc1",
+    "job_email": "",
+    "labeling_program": "cp2k",
+    "walltime_first_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
+    "walltime_second_job_h": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
+    "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+    "nb_mpi_per_node": [10, 10, 10, 10, 10, 10, 10, 10, 10, 10],
+    "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
+}
diff --git a/examples/diels_alder_ethene_13butadiene/R/001-training/used_input.json b/examples/diels_alder_ethene_13butadiene/R/001-training/used_input.json
@@ -0,0 +1,18 @@
+{
+    "user_machine_keyword_train": "a100_hpc1",
+    "user_machine_keyword_freeze": "v100_hpc1",
+    "user_machine_keyword_compress": "v100_hpc1",
+    "job_email": "",
+    "use_initial_datasets": true,
+    "use_extra_datasets": false,
+    "deepmd_model_version": 2.1,
+    "job_walltime_train_h": 2.0,
+    "mean_s_per_step": 0.018,
+    "start_lr": 0.001,
+    "stop_lr": 1e-06,
+    "decay_rate": 0.9172759353897796,
+    "decay_steps": 5000,
+    "decay_steps_fixed": false,
+    "numb_steps": 400000,
+    "numb_test": 0
+}
diff --git a/examples/diels_alder_ethene_13butadiene/R/used_input.json b/examples/diels_alder_ethene_13butadiene/R/used_input.json
@@ -0,0 +1,4 @@
+{
+    "systems_auto": ["product_free_300K", "product_OPES1D20_300K", "product_OPES1D50_300K", "product_OPES1D70_300K", "product_SMD_300K", "reactant_free_300K", "reactant_OPES1D20_300K", "reactant_OPES1D50_300K", "reactant_OPES1D70_300K", "reactant_SMD_300K"],
+    "nnp_count": 3
+}
diff --git a/...els_alder_ethene_13butadiene/R/user_files/1_product_OPES1D20_300K_labeling_XXXXX_hpc1.inp b/...els_alder_ethene_13butadiene/R/user_files/1_product_OPES1D20_300K_labeling_XXXXX_hpc1.inp
@@ -0,0 +1,135 @@
+@SET SYSNAME 1_labeling__R_PADDEDSTEP_
+
+&GLOBAL
+ PRINT_LEVEL LOW
+ PREFERRED_FFT_LIBRARY FFTW3
+ EXTENDED_FFT_LENGTHS FALSE
+ PROJECT ${SYSNAME}
+ RUN_TYPE ENERGY_FORCE
+ WALLTIME _R_WALLTIME_
+&END GLOBAL
+&FORCE_EVAL
+ METHOD QS
+ &DFT
+  BASIS_SET_FILE_NAME TZV2P-GTH
+  POTENTIAL_FILE_NAME GTH-BLYP
+  WFN_RESTART_FILE_NAME labeling__R_PADDEDSTEP_-SCF.wfn
+  CHARGE 0
+  MULTIPLICITY 1
+  &MGRID
+   SKIP_LOAD_BALANCE_DISTRIBUTED FALSE
+   CUTOFF [Ry] 600.0
+   REL_CUTOFF [Ry] 60.0
+   NGRIDS 4
+  &END MGRID
+  &SCF
+   MAX_SCF 20
+   EPS_SCF 1e-8
+   SCF_GUESS RESTART
+   &OUTER_SCF
+    EPS_SCF 1e-8
+    MAX_SCF 10
+   &END OUTER_SCF
+   &OT
+    PRECONDITIONER FULL_SINGLE_INVERSE
+    MINIMIZER DIIS
+    N_HISTORY_VEC 7
+   &END OT
+   &PRINT
+    &RESTART
+     FILENAME =labeling__R_PADDEDSTEP_-SCF.wfn
+     LOG_PRINT_KEY
+     BACKUP_COPIES 0
+     &EACH
+      QS_SCF 0
+      JUST_ENERGY 1
+     &END EACH
+     COMMON_ITERATION_LEVELS 1
+     ADD_LAST NUMERIC
+    &END RESTART
+    &RESTART_HISTORY OFF
+    &END RESTART_HISTORY
+   &END PRINT
+  &END SCF
+  &QS
+   METHOD GPW
+   EPS_DEFAULT 1.0E-14
+   EXTRAPOLATION ASPC
+   EXTRAPOLATION_ORDER 3
+  &END QS
+  &XC
+   DENSITY_CUTOFF 1.0E-10
+   GRADIENT_CUTOFF 1.0E-10
+   &XC_GRID
+    XC_SMOOTH_RHO NN50
+    XC_DERIV NN50_SMOOTH
+   &END XC_GRID
+   &XC_FUNCTIONAL BLYP
+   &END XC_FUNCTIONAL
+   &VDW_POTENTIAL
+    POTENTIAL_TYPE PAIR_POTENTIAL
+    &PAIR_POTENTIAL
+     R_CUTOFF 12.0
+     TYPE DFTD3
+     PARAMETER_FILE_NAME dftd3.dat
+     REFERENCE_FUNCTIONAL BLYP
+     VERBOSE_OUTPUT
+    &END PAIR_POTENTIAL
+   &END VDW_POTENTIAL
+  &END XC
+  &POISSON
+   POISSON_SOLVER WAVELET
+   PERIODIC NONE
+  &END POISSON
+ &END DFT
+ STRESS_TENSOR ANALYTICAL
+ &SUBSYS
+  &CELL
+   ABC [angstrom] _R_CELL_
+   ALPHA_BETA_GAMMA [deg] 90.0 90.0 90.0
+   MULTIPLE_UNIT_CELL 1 1 1
+   PERIODIC NONE
+   SYMMETRY ORTHORHOMBIC
+  &END CELL
+  &TOPOLOGY
+   &CENTER_COORDINATES TRUE
+   &END CENTER_COORDINATES
+   COORD_FILE_FORMAT XYZ
+   COORD_FILE_NAME labeling__R_PADDEDSTEP_.xyz
+  &END TOPOLOGY
+  &KIND C
+   BASIS_SET ORB TZV2P-GTH
+   POTENTIAL GTH-BLYP-q4
+  &END KIND
+  &KIND H
+   BASIS_SET ORB TZV2P-GTH
+   POTENTIAL GTH-BLYP-q1
+ &END KIND
+ &END SUBSYS
+ &PRINT
+  &PROGRAM_RUN_INFO
+   FILENAME =${SYSNAME}-Force_Eval.fe
+   LOG_PRINT_KEY
+   &EACH
+    JUST_ENERGY 1
+   &END EACH
+   ADD_LAST NUMERIC
+  &END PROGRAM_RUN_INFO
+  &FORCES
+   FILENAME =${SYSNAME}-Forces.for
+   LOG_PRINT_KEY
+   &EACH
+    JUST_ENERGY 1
+   &END EACH
+   ADD_LAST NUMERIC
+  &END
+  &STRESS_TENSOR
+   FILENAME =${SYSNAME}-Stress_Tensor.st
+   LOG_PRINT_KEY
+   &EACH
+    JUST_ENERGY 1
+   &END EACH
+   ADD_LAST NUMERIC
+  &END STRESS_TENSOR
+ &END PRINT
+&END FORCE_EVAL
diff --git a/...els_alder_ethene_13butadiene/R/user_files/1_product_OPES1D50_300K_labeling_XXXXX_hpc1.inp b/...els_alder_ethene_13butadiene/R/user_files/1_product_OPES1D50_300K_labeling_XXXXX_hpc1.inp
@@ -0,0 +1,135 @@
+@SET SYSNAME 1_labeling__R_PADDEDSTEP_
+
+&GLOBAL
+ PRINT_LEVEL LOW
+ PREFERRED_FFT_LIBRARY FFTW3
+ EXTENDED_FFT_LENGTHS FALSE
+ PROJECT ${SYSNAME}
+ RUN_TYPE ENERGY_FORCE
+ WALLTIME _R_WALLTIME_
+&END GLOBAL
+&FORCE_EVAL
+ METHOD QS
+ &DFT
+  BASIS_SET_FILE_NAME TZV2P-GTH
+  POTENTIAL_FILE_NAME GTH-BLYP
+  WFN_RESTART_FILE_NAME labeling__R_PADDEDSTEP_-SCF.wfn
+  CHARGE 0
+  MULTIPLICITY 1
+  &MGRID
+   SKIP_LOAD_BALANCE_DISTRIBUTED FALSE
+   CUTOFF [Ry] 600.0
+   REL_CUTOFF [Ry] 60.0
+   NGRIDS 4
+  &END MGRID
+  &SCF
+   MAX_SCF 20
+   EPS_SCF 1e-8
+   SCF_GUESS RESTART
+   &OUTER_SCF
+    EPS_SCF 1e-8
+    MAX_SCF 10
+   &END OUTER_SCF
+   &OT
+    PRECONDITIONER FULL_SINGLE_INVERSE
+    MINIMIZER DIIS
+    N_HISTORY_VEC 7
+   &END OT
+   &PRINT
+    &RESTART
+     FILENAME =labeling__R_PADDEDSTEP_-SCF.wfn
+     LOG_PRINT_KEY
+     BACKUP_COPIES 0
+     &EACH
+      QS_SCF 0
+      JUST_ENERGY 1
+     &END EACH
+     COMMON_ITERATION_LEVELS 1
+     ADD_LAST NUMERIC
+    &END RESTART
+    &RESTART_HISTORY OFF
+    &END RESTART_HISTORY
+   &END PRINT
+  &END SCF
+  &QS
+   METHOD GPW
+   EPS_DEFAULT 1.0E-14
+   EXTRAPOLATION ASPC
+   EXTRAPOLATION_ORDER 3
+  &END QS
+  &XC
+   DENSITY_CUTOFF 1.0E-10
+   GRADIENT_CUTOFF 1.0E-10
+   &XC_GRID
+    XC_SMOOTH_RHO NN50
+    XC_DERIV NN50_SMOOTH
+   &END XC_GRID
+   &XC_FUNCTIONAL BLYP
+   &END XC_FUNCTIONAL
+   &VDW_POTENTIAL
+    POTENTIAL_TYPE PAIR_POTENTIAL
+    &PAIR_POTENTIAL
+     R_CUTOFF 12.0
+     TYPE DFTD3
+     PARAMETER_FILE_NAME dftd3.dat
+     REFERENCE_FUNCTIONAL BLYP
+     VERBOSE_OUTPUT
+    &END PAIR_POTENTIAL
+   &END VDW_POTENTIAL
+  &END XC
+  &POISSON
+   POISSON_SOLVER WAVELET
+   PERIODIC NONE
+  &END POISSON
+ &END DFT
+ STRESS_TENSOR ANALYTICAL
+ &SUBSYS
+  &CELL
+   ABC [angstrom] _R_CELL_
+   ALPHA_BETA_GAMMA [deg] 90.0 90.0 90.0
+   MULTIPLE_UNIT_CELL 1 1 1
+   PERIODIC NONE
+   SYMMETRY ORTHORHOMBIC
+  &END CELL
+  &TOPOLOGY
+   &CENTER_COORDINATES TRUE
+   &END CENTER_COORDINATES
+   COORD_FILE_FORMAT XYZ
+   COORD_FILE_NAME labeling__R_PADDEDSTEP_.xyz
+  &END TOPOLOGY
+  &KIND C
+   BASIS_SET ORB TZV2P-GTH
+   POTENTIAL GTH-BLYP-q4
+  &END KIND
+  &KIND H
+   BASIS_SET ORB TZV2P-GTH
+   POTENTIAL GTH-BLYP-q1
+ &END KIND
+ &END SUBSYS
+ &PRINT
+  &PROGRAM_RUN_INFO
+   FILENAME =${SYSNAME}-Force_Eval.fe
+   LOG_PRINT_KEY
+   &EACH
+    JUST_ENERGY 1
+   &END EACH
+   ADD_LAST NUMERIC
+  &END PROGRAM_RUN_INFO
+  &FORCES
+   FILENAME =${SYSNAME}-Forces.for
+   LOG_PRINT_KEY
+   &EACH
+    JUST_ENERGY 1
+   &END EACH
+   ADD_LAST NUMERIC
+  &END
+  &STRESS_TENSOR
+   FILENAME =${SYSNAME}-Stress_Tensor.st
+   LOG_PRINT_KEY
+   &EACH
+    JUST_ENERGY 1
+   &END EACH
+   ADD_LAST NUMERIC
+  &END STRESS_TENSOR
+ &END PRINT
+&END FORCE_EVAL