AIMD NPT

dvc.lock

@@ -21337,3 +21337,206 @@ stages:
       hash: md5
       md5: 0a366e37c5368c0f3d9888f5d26a5d13
       size: 58176
+  AIMD_ConfigurationSelection:
+    cmd: zntrack run ipsuite.nodes.IndexSelection --name AIMD_ConfigurationSelection
+    deps:
+    - path: nodes/classical/AddData/atoms.h5
+      hash: md5
+      md5: 4b28c7c0a6ae386fce15e8c814259378
+      size: 19874075
+    - path: nodes/classical/AddData/node-meta.json
+      hash: md5
+      md5: e875cc934db72ea4d2b9d3be558e88d1
+      size: 48
+    params:
+      params.yaml:
+        AIMD_ConfigurationSelection:
+          indices:
+          - 2000
+    outs:
+    - path: nodes/AIMD/ConfigurationSelection/node-meta.json
+      hash: md5
+      md5: da71f5aa940cb81b46f4aea6f433b722
+      size: 48
+    - path: nodes/AIMD/ConfigurationSelection/selected_configurations.json
+      hash: md5
+      md5: 755d6c816224dec168bb7ef675f0733d
+      size: 49
+    - path: nodes/AIMD/ConfigurationSelection/selection.png
+      hash: md5
+      md5: 509cc04ed4e1e293ee81eb67105a6454
+      size: 25192
+  AIMD_CP2KSinglePoint:
+    cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name AIMD_CP2KSinglePoint
+    deps:
+    - path: GTH_BASIS_SETS
+      hash: md5
+      md5: 518e733a7344699cf0b4192bb97eb6a3
+      size: 119403
+    - path: GTH_POTENTIALS
+      hash: md5
+      md5: 3a35b03b26b8ba5cf6c1d849dba11f15
+      size: 128982
+    - path: dftd3.dat
+      hash: md5
+      md5: 88745bcc951a4bcdccc4d6bcfa78d105
+      size: 1959318
+    - path: nodes/AIMD/ConfigurationSelection/node-meta.json
+      hash: md5
+      md5: da71f5aa940cb81b46f4aea6f433b722
+      size: 48
+    - path: nodes/AIMD/ConfigurationSelection/selected_configurations.json
+      hash: md5
+      md5: 755d6c816224dec168bb7ef675f0733d
+      size: 49
+    - path: nodes/AIMD/ConfigurationSelection/selection.png
+      hash: md5
+      md5: 509cc04ed4e1e293ee81eb67105a6454
+      size: 25192
+    params:
+      config/cp2k.yaml:
+        force_eval:
+          method: quickstep
+          DFT:
+            mgrid:
+              cutoff: 800
+              rel_cutoff: 60
+              ngrids: 5
+            QS:
+              eps_filter_matrix: 0.0
+              eps_pgf_orb: 0.0001
+            SCF:
+              scf_guess: restart
+              max_scf: 100
+              eps_scf: 1e-06
+              OT:
+                minimizer: diis
+                preconditioner: full_single_inverse
+              outer_scf:
+                max_scf: 100
+                eps_scf: 1e-06
+              print:
+                restart:
+                  each:
+                    QS_SCF: 0
+            XC:
+              xc_functional:
+                becke97:
+                  parametrization: B97-3c
+                  scale_c: 1.0
+                  scale_x: 1.0
+              vdw_potential:
+                pair_potential:
+                  type: dftd3(bj)
+                  parameter_file_name: dftd3.dat
+                  reference_functional: B97-3c
+                  r_cutoff: 7.93766
+                  calculate_c9_term: true
+                  short_range_correction: true
+                potential_type: pair_potential
+            charge: 0
+            basis_set_file_name: GTH_BASIS_SETS
+            potential_file_name: GTH_POTENTIALS
+          subsys:
+            kind:
+              N:
+                basis_set: TZVP-GTH-q5
+                potential: GTH-PBE-q5
+              C:
+                basis_set: TZVP-GTH-q4
+                potential: GTH-PBE-q4
+              H:
+                basis_set: TZVP-GTH-q1
+                potential: GTH-PBE-q1
+              B:
+                basis_set: TZVP-GTH-q3
+                potential: GTH-PBE-q3
+              F:
+                basis_set: TZVP-GTH-q7
+                potential: GTH-PBE-q7
+    outs:
+    - path: nodes/AIMD/CP2KSinglePoint/atoms.h5
+      hash: md5
+      md5: 913b91fba4bf2e86ee5fc84efeb73667
+      size: 57448
+    - path: nodes/AIMD/CP2KSinglePoint/cp2k
+      hash: md5
+      md5: 97c3ffe7efca455b49b387f6ceb24389.dir
+      size: 12384695
+      nfiles: 3
+    - path: nodes/AIMD/CP2KSinglePoint/node-meta.json
+      hash: md5
+      md5: a61c58e291a27dd324ab6bb3b1ac6c68
+      size: 48
+  AIMD_ASEMD:
+    cmd: zntrack run ipsuite.nodes.ASEMD --name AIMD_ASEMD
+    deps:
+    - path: nodes/AIMD/CP2KSinglePoint/atoms.h5
+      hash: md5
+      md5: 913b91fba4bf2e86ee5fc84efeb73667
+      size: 57448
+    - path: nodes/AIMD/CP2KSinglePoint/cp2k
+      hash: md5
+      md5: 97c3ffe7efca455b49b387f6ceb24389.dir
+      size: 12384695
+      nfiles: 3
+    - path: nodes/AIMD/CP2KSinglePoint/node-meta.json
+      hash: md5
+      md5: a61c58e291a27dd324ab6bb3b1ac6c68
+      size: 48
+    - path: nodes/AIMD/ConfigurationSelection/node-meta.json
+      hash: md5
+      md5: da71f5aa940cb81b46f4aea6f433b722
+      size: 48
+    - path: nodes/AIMD/ConfigurationSelection/selected_configurations.json
+      hash: md5
+      md5: 755d6c816224dec168bb7ef675f0733d
+      size: 49
+    - path: nodes/AIMD/ConfigurationSelection/selection.png
+      hash: md5
+      md5: 509cc04ed4e1e293ee81eb67105a6454
+      size: 25192
+    params:
+      params.yaml:
+        AIMD_ASEMD:
+          data_id: -1
+          dump_rate: 1000
+          pop_last: false
+          repeat:
+          - 1
+          - 1
+          - 1
+          sampling_rate: 1
+          seed: 42
+          steps: 10
+          use_momenta: false
+          wrap: false
+        AIMD_ASEMD+thermostat:
+          pfactor: 54.273
+          pressure: 6.324e-07
+          temperature: 300
+          tetragonal_strain: true
+          time_step: 0.5
+          ttime: 2.4557
+    outs:
+    - path: nodes/AIMD/ASEMD/metrics_dict.csv
+      hash: md5
+      md5: 1dd6a0ba58ef2b30c206a55f882e0d80
+      size: 425
+    - path: nodes/AIMD/ASEMD/model
+      hash: md5
+      md5: 652bf93d8635ad1197ec31108f58f913.dir
+      size: 49513918
+      nfiles: 7
+    - path: nodes/AIMD/ASEMD/node-meta.json
+      hash: md5
+      md5: 7b0fa9212731103742ae910d828298a5
+      size: 48
+    - path: nodes/AIMD/ASEMD/steps_before_stopping.json
+      hash: md5
+      md5: 6bb61e3b7bce0931da574d19d1d82c88
+      size: 2
+    - path: nodes/AIMD/ASEMD/trajectory.h5
+      hash: md5
+      md5: 6900a0d6c1e56b10f74a2a7fda899503
+      size: 357632

dvc.yaml

@@ -179,7 +179,59 @@ plots:
     x_label: epochs
     y: val_loss
     y_label: validation loss
+- nodes/AIMD/ASEMD/metrics_dict.csv: {}
 stages:
+  AIMD_ASEMD:
+    cmd: zntrack run ipsuite.nodes.ASEMD --name AIMD_ASEMD
+    deps:
+    - nodes/AIMD/CP2KSinglePoint/atoms.h5
+    - nodes/AIMD/CP2KSinglePoint/cp2k
+    - nodes/AIMD/CP2KSinglePoint/node-meta.json
+    - nodes/AIMD/ConfigurationSelection/node-meta.json
+    - nodes/AIMD/ConfigurationSelection/selected_configurations.json
+    - nodes/AIMD/ConfigurationSelection/selection.png
+    metrics:
+    - nodes/AIMD/ASEMD/node-meta.json:
+        cache: false
+    - nodes/AIMD/ASEMD/steps_before_stopping.json:
+        cache: false
+    outs:
+    - nodes/AIMD/ASEMD/metrics_dict.csv
+    - nodes/AIMD/ASEMD/model
+    - nodes/AIMD/ASEMD/trajectory.h5
+    params:
+    - AIMD_ASEMD
+    - AIMD_ASEMD+thermostat
+  AIMD_CP2KSinglePoint:
+    cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name AIMD_CP2KSinglePoint
+    deps:
+    - GTH_BASIS_SETS
+    - GTH_POTENTIALS
+    - dftd3.dat
+    - nodes/AIMD/ConfigurationSelection/node-meta.json
+    - nodes/AIMD/ConfigurationSelection/selected_configurations.json
+    - nodes/AIMD/ConfigurationSelection/selection.png
+    metrics:
+    - nodes/AIMD/CP2KSinglePoint/node-meta.json:
+        cache: false
+    outs:
+    - nodes/AIMD/CP2KSinglePoint/atoms.h5
+    - nodes/AIMD/CP2KSinglePoint/cp2k
+    params:
+    - config/cp2k.yaml:
+  AIMD_ConfigurationSelection:
+    cmd: zntrack run ipsuite.nodes.IndexSelection --name AIMD_ConfigurationSelection
+    deps:
+    - nodes/classical/AddData/atoms.h5
+    - nodes/classical/AddData/node-meta.json
+    metrics:
+    - nodes/AIMD/ConfigurationSelection/node-meta.json:
+        cache: false
+    outs:
+    - nodes/AIMD/ConfigurationSelection/selected_configurations.json
+    - nodes/AIMD/ConfigurationSelection/selection.png
+    params:
+    - AIMD_ConfigurationSelection
   ML0_ConfigurationSelection:
     cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML0_ConfigurationSelection
     deps:
@@ -5122,6 +5174,31 @@ stages:
     - nodes/final_ensemble/PredictionMetrics/stress_deviatoric_df.csv
     - nodes/final_ensemble/PredictionMetrics/stress_df.csv
     - nodes/final_ensemble/PredictionMetrics/stress_hydrostatic_df.csv
+  final_ensemble_PredictionMetrics_1:
+    cmd: zntrack run ipsuite.nodes.PredictionMetrics --name final_ensemble_PredictionMetrics_1
+    deps:
+    - nodes/final_ensemble/Prediction_1/atoms.h5
+    - nodes/final_ensemble/Prediction_1/node-meta.json
+    metrics:
+    - nodes/final_ensemble/PredictionMetrics_1/deviat_stress.json:
+        cache: false
+    - nodes/final_ensemble/PredictionMetrics_1/energy.json:
+        cache: false
+    - nodes/final_ensemble/PredictionMetrics_1/forces.json:
+        cache: false
+    - nodes/final_ensemble/PredictionMetrics_1/hydro_stress.json:
+        cache: false
+    - nodes/final_ensemble/PredictionMetrics_1/node-meta.json:
+        cache: false
+    - nodes/final_ensemble/PredictionMetrics_1/stress.json:
+        cache: false
+    outs:
+    - nodes/final_ensemble/PredictionMetrics_1/energy_df.csv
+    - nodes/final_ensemble/PredictionMetrics_1/forces_df.csv
+    - nodes/final_ensemble/PredictionMetrics_1/plots
+    - nodes/final_ensemble/PredictionMetrics_1/stress_deviatoric_df.csv
+    - nodes/final_ensemble/PredictionMetrics_1/stress_df.csv
+    - nodes/final_ensemble/PredictionMetrics_1/stress_hydrostatic_df.csv
   final_ensemble_Prediction_1:
     cmd: zntrack run ipsuite.nodes.Prediction --name final_ensemble_Prediction_1
     deps:
@@ -5182,33 +5259,8 @@ stages:
     - nodes/final_ensemble/MLModel/node-meta.json
     - nodes/final_ensemble/MLModel/train_atoms.extxyz
     - nodes/final_ensemble/MLModel/val_atoms.extxyz
-    outs:
-    - nodes/final_ensemble/Prediction_1/atoms.h5
     metrics:
     - nodes/final_ensemble/Prediction_1/node-meta.json:
         cache: false
-  final_ensemble_PredictionMetrics_1:
-    cmd: zntrack run ipsuite.nodes.PredictionMetrics --name final_ensemble_PredictionMetrics_1
-    deps:
-    - nodes/final_ensemble/Prediction_1/atoms.h5
-    - nodes/final_ensemble/Prediction_1/node-meta.json
     outs:
-    - nodes/final_ensemble/PredictionMetrics_1/energy_df.csv
-    - nodes/final_ensemble/PredictionMetrics_1/forces_df.csv
-    - nodes/final_ensemble/PredictionMetrics_1/plots
-    - nodes/final_ensemble/PredictionMetrics_1/stress_deviatoric_df.csv
-    - nodes/final_ensemble/PredictionMetrics_1/stress_df.csv
-    - nodes/final_ensemble/PredictionMetrics_1/stress_hydrostatic_df.csv
-    metrics:
-    - nodes/final_ensemble/PredictionMetrics_1/deviat_stress.json:
-        cache: false
-    - nodes/final_ensemble/PredictionMetrics_1/energy.json:
-        cache: false
-    - nodes/final_ensemble/PredictionMetrics_1/forces.json:
-        cache: false
-    - nodes/final_ensemble/PredictionMetrics_1/hydro_stress.json:
-        cache: false
-    - nodes/final_ensemble/PredictionMetrics_1/node-meta.json:
-        cache: false
-    - nodes/final_ensemble/PredictionMetrics_1/stress.json:
-        cache: false
+    - nodes/final_ensemble/Prediction_1/atoms.h5

main.py

@@ -55,6 +55,37 @@
         sampling_rate=10,
     )
 
+thermostat = ips.calculators.NPTThermostat(
+        time_step=0.5,
+        temperature=300,
+        pressure=6.324e-07, # 1.01325 * units.bar,
+        ttime=2.4557, # 25 * units.fs,
+        pfactor=54.273, # (75 * units.fs) ** 2,
+        tetragonal_strain=True,
+    )
+
+with project.group("AIMD") as aimd_grp:
+    start_conf = ips.configuration_selection.IndexSelection(
+        data.atoms,
+        indices=[2000,]
+    )
+
+    aimd_model = ips.calculators.CP2KSinglePoint(
+        data=start_conf.atoms,
+        cp2k_params="config/cp2k.yaml",
+        cp2k_files=["GTH_BASIS_SETS", "GTH_POTENTIALS", "dftd3.dat"],
+    )
+
+    aimd = ips.calculators.ASEMD(
+        data=start_conf.atoms,
+        data_id=-1,
+        model=aimd_model,
+        thermostat=thermostat,
+        steps=10_000,
+        sampling_rate=1,
+    )
+
+
 with project.group("ML0"):
     kernel_selection = ips.models.apax.BatchKernelSelection(
         data=train_data.excluded_atoms,
@@ -536,4 +567,4 @@
     prediction = ips.analysis.Prediction(data=train_data, model=model)
     metrics = ips.analysis.PredictionMetrics(data=prediction)
 
-project.build(nodes=[final])
+project.build(nodes=[aimd_grp])

nodes/AIMD/ASEMD/.gitignore

@@ -0,0 +1,3 @@
+/trajectory.h5
+/model
+/metrics_dict.csv

nodes/AIMD/ASEMD/node-meta.json

@@ -0,0 +1 @@
+{"uuid": "85690b32-3783-4df7-99df-facf4fa72fa7"}

nodes/AIMD/ASEMD/steps_before_stopping.json

@@ -0,0 +1 @@
+-1

nodes/AIMD/CP2KSinglePoint/.gitignore

@@ -0,0 +1,2 @@
+/cp2k
+/atoms.h5

nodes/AIMD/CP2KSinglePoint/node-meta.json

@@ -0,0 +1 @@
+{"uuid": "e0f6d873-64a4-4978-9c86-140653846ce9"}

nodes/AIMD/ConfigurationSelection/.gitignore

@@ -0,0 +1,2 @@
+/selected_configurations.json
+/selection.png

nodes/AIMD/ConfigurationSelection/node-meta.json

@@ -0,0 +1 @@
+{"uuid": "df38abb8-600a-4b2e-98e2-ce1836470ba6"}