Merge branch 'abinit_workflows_dfpt_shg' of github.com:VicTrqt/atomate2 into abinit_workflows_dfpt_shg

srun with options + autoparal 1

Author: VicTrqt

Diff for: src/atomate2/abinit/flows/dfpt.py

@@ -109,13 +109,15 @@ def make(
         static_job = update_user_kpoints_settings(  static_job, {"grid_density": 3000})
         static_job = update_user_abinit_settings(   static_job, {   'nstep': 500,
                                                                     'toldfe': 1e-22,
-                                                                    'chksymbreak': '0'}) # TO DO: modify to 500
+                                                                    'autoparal': 1,
+                                                                    'npfft': 1,
+                                                                    'chksymbreak': '0'})
         jobs = [static_job]
 
         if self.ddk_maker:
             # generate the perturbations for the DDK calculations
             ddk_perts = generate_ddk_perts(
-                gsinput=static_job.output.abinit_input,  # TODO: is that possible?
+                gsinput=static_job.output.abinit_input,
                 use_symmetries=self.use_ddk_sym,
             )
             jobs.append(ddk_perts)
@@ -131,7 +133,7 @@ def make(
         if self.dde_maker:
             # generate the perturbations for the DDE calculations
             dde_perts = generate_dde_perts(
-                gsinput=static_job.output.abinit_input,  # TODO: is that possible?
+                gsinput=static_job.output.abinit_input,
                 use_symmetries=self.use_dde_sym,
             )
             jobs.append(dde_perts)
@@ -147,7 +149,7 @@ def make(
         if self.dte_maker:
             # generate the perturbations for the DTE calculations
             dte_perts = generate_dte_perts(
-                gsinput=static_job.output.abinit_input,  # TODO: is that possible?
+                gsinput=static_job.output.abinit_input,
                 skip_permutations=self.dte_skip_permutations,
                 phonon_pert=self.dte_phonon_pert,
                 ixc=self.dte_ixc,

Diff for: src/atomate2/abinit/jobs/response.py

@@ -256,6 +256,8 @@ def generate_dte_perts(
         from pseudos.
     """
     # Call Abinit to get the list of irreducible perturbations
+    gsinput = gsinput.deepcopy()
+    gsinput.pop_vars(['autoparal', 'npfft'])
     perts = gsinput.abiget_irred_dteperts(
         phonon_pert=phonon_pert, ixc=ixc
     )  # TODO: quid manager?

Diff for: src/atomate2/abinit/run.py

@@ -11,8 +11,8 @@
 from atomate2 import SETTINGS
 from atomate2.abinit.utils.common import (
     INPUT_FILE_NAME,
-    MRGDDB_INPUT_FILE_NAME,
     LOG_FILE_NAME,
+    MRGDDB_INPUT_FILE_NAME,
     STDERR_FILE_NAME,
 )
 
@@ -34,8 +34,11 @@ def run_abinit(
     """Run ABINIT."""
     abinit_cmd = abinit_cmd or SETTINGS.ABINIT_CMD
     mpirun_cmd = mpirun_cmd or SETTINGS.ABINIT_MPIRUN_CMD
+    command = []
+    if mpirun_cmd:
+        command.extend(mpirun_cmd.split())
+    command.append(abinit_cmd)
     start_time = start_time or time.time()
-    command = [mpirun_cmd, abinit_cmd] if mpirun_cmd is not None else [abinit_cmd]
 
     max_end_time = 0.0
     if wall_time is not None:
@@ -78,9 +81,12 @@ def run_mrgddb(
     """Run mrgddb."""
     mrgddb_cmd = mrgddb_cmd or SETTINGS.ABINIT_MRGDDB_CMD
     mpirun_cmd = mpirun_cmd or SETTINGS.ABINIT_MPIRUN_CMD
+    command = []
+    if mpirun_cmd:
+        command.extend(mpirun_cmd.split())
+        command.extend(["-n", "1"])
+    command.extend([mrgddb_cmd, "--nostrict"])
     start_time = start_time or time.time()
-    command = [mpirun_cmd, "-n", "1", mrgddb_cmd, "--nostrict"] if mpirun_cmd is not None else [mrgddb_cmd]
-
 
     max_end_time = 0.0
     if wall_time is not None:
@@ -92,11 +98,13 @@ def run_mrgddb(
         command.extend(["--timelimit", time2slurm(mrgddb_timelimit)])
         max_end_time = start_time + wall_time
 
-    #command.append("< "+MRGDDB_INPUT_FILE_NAME)
+    # command.append("< "+MRGDDB_INPUT_FILE_NAME)
 
     status = "completed"
 
-    with open(MRGDDB_INPUT_FILE_NAME, "r") as stdin, open(LOG_FILE_NAME, "w") as stdout, open(STDERR_FILE_NAME, "w") as stderr:
+    with open(MRGDDB_INPUT_FILE_NAME) as stdin, open(
+        LOG_FILE_NAME, "w"
+    ) as stdout, open(STDERR_FILE_NAME, "w") as stderr:
         process = subprocess.Popen(command, stdin=stdin, stdout=stdout, stderr=stderr)
 
         if wall_time is not None: