Ab inito MD

.dvc/config

@@ -1,8 +1,8 @@
 [core]
     remote = origin
 ['remote "origin"']
-    url = s3://dvc/IPS-DMSO
-    endpointurl = https://minio.pythonf.net
-    access_key_id = DMSOgzb6NSeJZRIb
-    secret_access_key = qSZqFqYtR98hs1nS8avAZZ9xDHrNWD3z
+    url = s3://public/paper/dmso2023/
+    endpointurl = https://minio.icp.uni-stuttgart.de
+    access_key_id = public_eip8waishae6ies
+    secret_access_key = OoCiedah9aw9Pui8mie7phahlatie7oi
 

cp2k_md.yaml

@@ -0,0 +1,76 @@
+global:
+  run_type: md
+force_eval:
+  method: quickstep
+  DFT:
+    mgrid:
+      cutoff: 600.0
+      rel_cutoff: 80.0
+      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:
+        _: BLYP
+      vdw_potential:
+        pair_potential:
+          type: DFTD3
+          parameter_file_name: dftd3.dat
+          reference_functional: BLYP
+          r_cutoff: 18
+        potential_type: pair_potential
+    basis_set_file_name: BASIS_MOLOPT
+    potential_file_name: GTH_POTENTIALS
+  subsys:
+    kind:
+      O:
+        basis_set: TZV2P-MOLOPT-GTH-q6
+        potential: GTH-BLYP-q6
+      C:
+        basis_set: TZV2P-MOLOPT-GTH-q4
+        potential: GTH-BLYP-q4
+      H:
+        basis_set: TZV2P-MOLOPT-GTH-q1
+        potential: GTH-BLYP-q1
+      S:
+        basis_set: TZV2P-MOLOPT-GTH-q6
+        potential: GTH-BLYP-q6
+motion:
+  print:
+    trajectory:
+      each:
+        md: 1
+    forces:
+      each:
+        md: 1
+    stress:
+      each:
+        md: 1
+    restart:
+      each:
+        md: 1
+  md:
+    ensemble: nvt
+    temperature: 360
+    timestep: 0.5
+    steps: 12000
+    thermostat:
+      type: nose
+      region: massive
+      nose:
+        timecon: 100

dvc.lock

@@ -25029,3 +25029,110 @@ stages:
       hash: md5
       md5: bf2e9cc956893dd0d1eda9eb70864bed
       size: 4875
+  CP2KYaml:
+    cmd: zntrack run ipsuite.nodes.CP2KYaml --name CP2KYaml
+    deps:
+    - path: nodes/ASEGeoOpt/model_outs
+      hash: md5
+      md5: 55a17d4cf10898236beac4f2d757f2b4.dir
+      size: 89601466
+      nfiles: 7
+    - path: nodes/ASEGeoOpt/node-meta.json
+      hash: md5
+      md5: 336193404ed866dfebe5a4c56f8ef2f8
+      size: 48
+    - path: nodes/ASEGeoOpt/trajectory.h5
+      hash: md5
+      md5: ea5b960f96c3f1f8cd9328fb1ea918f5
+      size: 1410008
+    params:
+      params.yaml:
+        CP2KYaml:
+          data_id: -1
+      cp2k_md.yaml:
+        force_eval:
+          method: quickstep
+          DFT:
+            mgrid:
+              cutoff: 600.0
+              rel_cutoff: 80.0
+              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:
+                _: BLYP
+              vdw_potential:
+                pair_potential:
+                  type: DFTD3
+                  parameter_file_name: dftd3.dat
+                  reference_functional: BLYP
+                  r_cutoff: 18
+                potential_type: pair_potential
+            basis_set_file_name: BASIS_MOLOPT
+            potential_file_name: GTH_POTENTIALS
+          subsys:
+            kind:
+              O:
+                basis_set: TZV2P-MOLOPT-GTH-q6
+                potential: GTH-BLYP-q6
+              C:
+                basis_set: TZV2P-MOLOPT-GTH-q4
+                potential: GTH-BLYP-q4
+              H:
+                basis_set: TZV2P-MOLOPT-GTH-q1
+                potential: GTH-BLYP-q1
+              S:
+                basis_set: TZV2P-MOLOPT-GTH-q6
+                potential: GTH-BLYP-q6
+        global:
+          run_type: md
+        motion:
+          print:
+            trajectory:
+              each:
+                md: 1
+            forces:
+              each:
+                md: 1
+            stress:
+              each:
+                md: 1
+            restart:
+              each:
+                md: 1
+          md:
+            ensemble: nvt
+            temperature: 360
+            timestep: 0.5
+            steps: 12000
+            thermostat:
+              type: nose
+              region: massive
+              nose:
+                timecon: 100
+    outs:
+    - path: nodes/CP2KYaml/cp2k
+      hash: md5
+      md5: 3edda8bb305bf54797df5f60d2e2b137.dir
+      size: 1483817170
+      nfiles: 38
+    - path: nodes/CP2KYaml/node-meta.json
+      hash: md5
+      md5: 262e7d278116ccd0377b3a40b3b4c116
+      size: 48