Fpop support for CP2K (#27)

* Fpop support for CP2K (Bohrium) * Update and rename preprunvasp.py to prepruncp2k.py * Update cp2k.py Throw error if user does not specify command. Remove the last blank line * Add Unit test(UT) for Cp2k * Update cp2k.py deleted blank line again * Update test_cp2k_inputs.py * Update test_prep_cp2k.py * Update setup.py * Update requirements.txt * Update test_run_cp2k.py * Update test_prep_cp2k.py * Update test_cp2k_inputs.py * Update cp2k.py
deepmodeling · Jun 27, 2024 · 00d7497 · 00d7497
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diff --git a/examples/cp2k/POSCAR-1 b/examples/cp2k/POSCAR-1
@@ -0,0 +1,10 @@
+generated by phonopy
+   1.0
+     2.7523087463752396    0.0000000000000000    0.0000000000000000
+     0.0000000000000000    2.7523087463752396    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    2.7523087463752396
+Na
+   2
+Direct
+  0.0000000000000000  0.0000000000000000  0.0000000000000000
+  0.5000000000000000  0.5000000000000000  0.5000000000000000
diff --git a/examples/cp2k/POSCAR-2 b/examples/cp2k/POSCAR-2
@@ -0,0 +1,10 @@
+generated by phonopy
+   1.0
+     2.7236843018032482    0.0000000000000000    0.0000000000000000
+     0.0000000000000000    2.7236843018032482    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    2.7236843018032482
+Na
+   2
+Direct
+  0.0000000000000000  0.0000000000000000  0.0000000000000000
+  0.5000000000000000  0.5000000000000000  0.5000000000000000
diff --git a/examples/cp2k/POSCAR-3 b/examples/cp2k/POSCAR-3
@@ -0,0 +1,10 @@
+generated by phonopy
+   1.0
+     2.6974919917106432    0.0000000000000000    0.0000000000000000
+     0.0000000000000000    2.6974919917106432    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    2.6974919917106432
+Na
+   2
+Direct
+  0.5000000000000000  0.5000000000000000  0.5000000000000000
+  0.0000000000000000  0.0000000000000000  0.0000000000000000
diff --git a/examples/cp2k/input.inp b/examples/cp2k/input.inp
@@ -0,0 +1,71 @@
+#Generated by Multiwfn
+&GLOBAL
+  PROJECT POSCAR-1
+  PRINT_LEVEL LOW
+  RUN_TYPE ENERGY_FORCE
+&END GLOBAL
+
+&FORCE_EVAL
+  METHOD Quickstep
+  &SUBSYS
+    &CELL
+	  @INCLUDE CELL_PARAMETER
+      PERIODIC XYZ #Direction(s) of applied PBC (geometry aspect)
+    &END CELL
+    &COORD
+      @INCLUDE coord.xyz
+    &END COORD
+    &KIND Na
+      ELEMENT Na
+      BASIS_SET DZVP-MOLOPT-SR-GTH-q9
+      POTENTIAL GTH-PBE
+    &END KIND
+  &END SUBSYS
+
+  &DFT
+    BASIS_SET_FILE_NAME  BASIS_MOLOPT
+    POTENTIAL_FILE_NAME  POTENTIAL
+#   WFN_RESTART_FILE_NAME POSCAR-1-RESTART.wfn
+    CHARGE    0 #Net charge
+    MULTIPLICITY    1 #Spin multiplicity
+    &QS
+      EPS_DEFAULT 1.0E-12 #Set all EPS_xxx to values such that the energy will be correct up to this value
+    &END QS
+    &POISSON
+      PERIODIC XYZ #Direction(s) of PBC for calculating electrostatics
+      PSOLVER PERIODIC #The way to solve Poisson equation
+    &END POISSON
+    &XC
+      &XC_FUNCTIONAL PBE
+      &END XC_FUNCTIONAL
+    &END XC
+    &MGRID
+      CUTOFF  400
+      REL_CUTOFF  55
+    &END MGRID
+    &SCF
+      MAX_SCF 25 #Maximum number of steps of inner SCF
+      EPS_SCF 1.0E-06 #Convergence threshold of density matrix of inner SCF
+#     SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as initial guess
+      &OT
+        PRECONDITIONER FULL_ALL #Usually best but expensive for large system. Cheaper: FULL_SINGLE_INVERSE and FULL_KINETIC
+        MINIMIZER DIIS #CG is worth to consider in difficult cases
+        LINESEARCH 2PNT #1D line search algorithm for CG. 2PNT is default, 3PNT is better but more costly. GOLD is best but very expensive
+        ALGORITHM STRICT #Algorithm of OT. Can be STRICT (default) or IRAC
+      &END OT
+      &OUTER_SCF
+        MAX_SCF 20 #Maximum number of steps of outer SCF
+        EPS_SCF 1.0E-06 #Convergence threshold of outer SCF
+      &END OUTER_SCF
+      &PRINT
+        &RESTART #Note: Use "&RESTART OFF" can prevent generating .wfn file
+          BACKUP_COPIES 0 #Maximum number of backup copies of wfn file. 0 means never
+        &END RESTART
+      &END PRINT
+    &END SCF
+  &END DFT
+  &PRINT
+    &FORCES ON #Print atomic forces
+    &END FORCES
+  &END PRINT
+&END FORCE_EVAL
diff --git a/examples/cp2k/prepruncp2k.py b/examples/cp2k/prepruncp2k.py
@@ -0,0 +1,97 @@
+from dflow import (
+    Workflow,
+    Step,
+    upload_artifact,
+    download_artifact,
+    InputArtifact,
+    OutputArtifact,
+    ShellOPTemplate,
+)
+from dflow.python import (
+    PythonOPTemplate,
+    OP,
+    OPIO,
+    OPIOSign,
+    Artifact,
+    TransientError,
+    FatalError,
+    BigParameter,
+    upload_packages,
+)
+from pathlib import Path
+import fpop
+from fpop.cp2k import PrepCp2k,Cp2kInputs,RunCp2k
+from fpop.preprun_fp import PrepRunFp
+from dflow.plugins.dispatcher import DispatcherExecutor
+
+prep_template_config={}
+prep_step_config={}
+run_template_config={}
+run_slice_config={}
+run_step_config={
+        "executor":{
+            "type": "dispatcher",
+            "machine_dict":{
+                "batch_type": "Bohrium",
+                "context_type": "Bohrium",
+                "remote_profile": {
+                    "input_data": {
+                        "job_type": "container",
+                        "platform": "ali",
+                        "scass_type": "c16_m32_cpu",
+                        }
+                    }
+                }
+            }
+    }
+prep_image_config={}
+run_image_config={
+    "command": "ulimit -s unlimited && ulimit -m unlimited && mpirun -n 16 --allow-run-as-root --oversubscribe cp2k.popt -i input.inp",
+    }
+upload_python_packages=list(fpop.__path__)
+
+steps = PrepRunFp(
+    "prep-run-cp2k",
+    PrepCp2k,
+    RunCp2k,
+    "registry.dp.tech/dptech/prod-15842/ubuntu:22.04-py3.10-ase",
+    "registry.dp.tech/dptech/prod-25571/initreaction:cp2k0410",
+    prep_template_config,
+    prep_step_config,
+    run_template_config,
+    run_slice_config,
+    run_step_config,
+    upload_python_packages, 
+)
+
+confs = ["POSCAR-1","POSCAR-2","POSCAR-3"]
+
+
+cp2k_inputs = Cp2kInputs('input.inp') # input files
+prep_run_step = Step(
+    'prep-run-step', 
+    template = steps,
+    parameters = {
+        'type_map' : ["Na"],
+        'prep_image_config' : prep_image_config,
+        'run_image_config' : run_image_config,
+        "log_name" : "output.log",
+        'inputs' : cp2k_inputs,
+        'optional_input' : {"conf_format":"vasp/poscar"},
+        'backward_list' : ["output.log"],
+    },
+    artifacts = {
+        "confs" : upload_artifact(confs),
+    },
+)
+
+wf = Workflow(name="prepruncp2k")
+wf.add(prep_run_step)
+wf.submit()
+
+import time
+while wf.query_status() in ["Pending", "Running"]:
+    time.sleep(4)
+assert(wf.query_status() == 'Succeeded')
+step = wf.query_step(name="prep-run-step")[0]
+download_artifact(step.outputs.artifacts["backward_dirs"])