Merge pull request mala-project#595 from RandomDefaultUser/temp_file_qe

Implemented `tempfile` for TEM

external_modules/total_energy_module/total_energy.f90

@@ -1,4 +1,4 @@
-SUBROUTINE initialize(y_planes_in, calculate_eigts_in)
+SUBROUTINE initialize(file_name, y_planes_in, calculate_eigts_in)
   !----------------------------------------------------------------------------
   !  Derived from Quantum Espresso code
   !! author: Paolo Giannozzi
@@ -29,6 +29,7 @@ SUBROUTINE initialize(y_planes_in, calculate_eigts_in)
   LOGICAL, INTENT(IN), OPTIONAL :: calculate_eigts_in
   LOGICAL :: calculate_eigts = .false.
   INTEGER, INTENT(IN), OPTIONAL :: y_planes_in
+  CHARACTER(len=256), INTENT(IN) :: file_name
     ! Parse optional arguments.
   IF (PRESENT(calculate_eigts_in)) THEN
     calculate_eigts = calculate_eigts_in
@@ -45,7 +46,7 @@ SUBROUTINE initialize(y_planes_in, calculate_eigts_in)
   !
   CALL environment_start ( 'PWSCF' )
   !
-  CALL read_input_file ('PW', 'mala.pw.scf.in' )
+  CALL read_input_file ('PW', file_name )
   CALL run_pwscf_setup ( exit_status, calculate_eigts)
 
   print *, "Setup completed"

mala/descriptors/bispectrum.py

@@ -1,7 +1,6 @@
 """Bispectrum descriptor class."""
 
 import os
-import tempfile
 
 import ase
 import ase.io
@@ -963,21 +962,21 @@ def __compute_ui(self, nr_atoms, atoms_cutoff, distances_cutoff, grid):
                     )
                     jju1 += 1
                 if jju_outer in self.__index_u1_symmetry_pos:
-                    ulist_r_ij[
-                        :, self.__index_u1_symmetry_pos[jju2]
-                    ] = ulist_r_ij[:, self.__index_u_symmetry_pos[jju2]]
-                    ulist_i_ij[
-                        :, self.__index_u1_symmetry_pos[jju2]
-                    ] = -ulist_i_ij[:, self.__index_u_symmetry_pos[jju2]]
+                    ulist_r_ij[:, self.__index_u1_symmetry_pos[jju2]] = (
+                        ulist_r_ij[:, self.__index_u_symmetry_pos[jju2]]
+                    )
+                    ulist_i_ij[:, self.__index_u1_symmetry_pos[jju2]] = (
+                        -ulist_i_ij[:, self.__index_u_symmetry_pos[jju2]]
+                    )
                     jju2 += 1
 
                 if jju_outer in self.__index_u1_symmetry_neg:
-                    ulist_r_ij[
-                        :, self.__index_u1_symmetry_neg[jju3]
-                    ] = -ulist_r_ij[:, self.__index_u_symmetry_neg[jju3]]
-                    ulist_i_ij[
-                        :, self.__index_u1_symmetry_neg[jju3]
-                    ] = ulist_i_ij[:, self.__index_u_symmetry_neg[jju3]]
+                    ulist_r_ij[:, self.__index_u1_symmetry_neg[jju3]] = (
+                        -ulist_r_ij[:, self.__index_u_symmetry_neg[jju3]]
+                    )
+                    ulist_i_ij[:, self.__index_u1_symmetry_neg[jju3]] = (
+                        ulist_i_ij[:, self.__index_u_symmetry_neg[jju3]]
+                    )
                     jju3 += 1
 
             # This emulates add_uarraytot.

mala/descriptors/descriptor.py

@@ -228,33 +228,36 @@ def setup_lammps_tmp_files(self, lammps_type, outdir):
             Type of descriptor calculation (e.g. bgrid for bispectrum)
         outdir: str
             Directory where lammps files are kept
-        
+
         Returns
         -------
         None
         """
         if get_rank() == 0:
             prefix_inp_str = "lammps_" + lammps_type + "_input"
             prefix_log_str = "lammps_" + lammps_type + "_log"
-            lammps_tmp_input_file=tempfile.NamedTemporaryFile(
+            lammps_tmp_input_file = tempfile.NamedTemporaryFile(
                 delete=False, prefix=prefix_inp_str, suffix="_.tmp", dir=outdir
             )
             self.lammps_temporary_input = lammps_tmp_input_file.name
             lammps_tmp_input_file.close()
 
-            lammps_tmp_log_file=tempfile.NamedTemporaryFile(
+            lammps_tmp_log_file = tempfile.NamedTemporaryFile(
                 delete=False, prefix=prefix_log_str, suffix="_.tmp", dir=outdir
             )
             self.lammps_temporary_log = lammps_tmp_log_file.name
             lammps_tmp_log_file.close()
         else:
-            self.lammps_temporary_input=None
-            self.lammps_temporary_log=None
+            self.lammps_temporary_input = None
+            self.lammps_temporary_log = None
 
         if self.parameters._configuration["mpi"]:
-            self.lammps_temporary_input = get_comm().bcast(self.lammps_temporary_input, root=0)
-            self.lammps_temporary_log = get_comm().bcast(self.lammps_temporary_log, root=0)
-
+            self.lammps_temporary_input = get_comm().bcast(
+                self.lammps_temporary_input, root=0
+            )
+            self.lammps_temporary_log = get_comm().bcast(
+                self.lammps_temporary_log, root=0
+            )
 
     # Calculations
     ##############

mala/interfaces/ase_calculator.py

@@ -3,7 +3,7 @@
 from ase.calculators.calculator import Calculator, all_changes
 
 from mala import Parameters, Network, DataHandler, Predictor, LDOS
-from mala.common.parallelizer import barrier, parallel_warn
+from mala.common.parallelizer import barrier, parallel_warn, get_rank, get_comm
 
 
 class MALA(Calculator):
@@ -154,28 +154,23 @@ def calculate(
         # Get the LDOS from the NN.
         ldos = self.predictor.predict_for_atoms(atoms)
 
-        # forces = np.zeros([len(atoms), 3], dtype=np.float64)
-
-        # If an MPI environment is detected, ASE will use it for writing.
-        # Therefore we have to do this before forking.
-        self.data_handler.target_calculator.write_tem_input_file(
-            atoms,
-            self.data_handler.target_calculator.qe_input_data,
-            self.data_handler.target_calculator.qe_pseudopotentials,
-            self.data_handler.target_calculator.grid_dimensions,
-            self.data_handler.target_calculator.kpoints,
-        )
-
+        # Use the LDOS determined DOS and density to get energy and forces.
         ldos_calculator: LDOS = self.data_handler.target_calculator
-
         ldos_calculator.read_from_array(ldos)
+        self.results["energy"] = ldos_calculator.total_energy
         energy, self.last_energy_contributions = (
             ldos_calculator.get_total_energy(return_energy_contributions=True)
         )
+        self.last_energy_contributions = (
+            ldos_calculator._density_calculator.total_energy_contributions.copy()
+        )
+        self.last_energy_contributions["e_band"] = ldos_calculator.band_energy
+        self.last_energy_contributions["e_entropy_contribution"] = (
+            ldos_calculator.entropy_contribution
+        )
         barrier()
 
-        # Use the LDOS determined DOS and density to get energy and forces.
-        self.results["energy"] = energy
+        # forces = np.zeros([len(atoms), 3], dtype=np.float64)
         # if "forces" in properties:
         #     self.results["forces"] = forces
 

mala/targets/density.py

@@ -1,5 +1,6 @@
 """Electronic density calculation class."""
 
+import os.path
 import time
 
 from ase.units import Rydberg, Bohr, m
@@ -16,6 +17,8 @@
     parallel_warn,
     barrier,
     get_size,
+    get_comm,
+    get_rank,
 )
 from mala.targets.target import Target
 from mala.targets.cube_parser import read_cube, write_cube
@@ -406,7 +409,7 @@ def read_from_cube(self, path, units="1/Bohr^3", **kwargs):
         printout("Reading density from .cube file ", path, min_verbosity=0)
         # automatically convert units if they are None since cube files take atomic units
         if units is None:
-            units="1/Bohr^3"
+            units = "1/Bohr^3"
         if units != "1/Bohr^3":
             printout(
                 "The expected units for the density from cube files are 1/Bohr^3\n"
@@ -960,12 +963,14 @@ def __setup_total_energy_module(
             else:
                 kpoints = self.kpoints
 
-            self.write_tem_input_file(
+            tem_input_name = self.write_tem_input_file(
                 atoms_Angstrom,
                 qe_input_data,
                 qe_pseudopotentials,
                 self.grid_dimensions,
                 kpoints,
+                get_comm(),
+                get_rank(),
             )
 
         # initialize the total energy module.
@@ -984,8 +989,22 @@ def __setup_total_energy_module(
             )
             barrier()
             t0 = time.perf_counter()
-            te.initialize(self.y_planes)
+
+            # We have to make sure we have the correct format for the file.
+            # QE expects the file without a path, and with a fixed length.
+            # I chose 256 for this length, simply to have some space in case
+            # we need it at some point (i.e., the tempfile format changes).
+            tem_input_name_qe = os.path.basename(tem_input_name)
+            tem_input_name_qe = tem_input_name_qe + " " * (
+                256 - len(tem_input_name_qe)
+            )
+            te.initialize(tem_input_name_qe, self.y_planes)
             barrier()
+
+            # Right after setup we can delete the file.
+            if get_rank() == 0:
+                os.remove(tem_input_name)
+
             printout(
                 "Total energy module: Time used by total energy initialization: {:.8f}s".format(
                     time.perf_counter() - t0

mala/targets/target.py

@@ -4,6 +4,7 @@
 import itertools
 import json
 import os
+import tempfile
 
 from ase.neighborlist import NeighborList
 from ase.units import Rydberg, kB
@@ -14,7 +15,12 @@
 from scipy.integrate import simpson
 
 from mala.common.parameters import Parameters, ParametersTargets
-from mala.common.parallelizer import printout, parallel_warn, get_rank
+from mala.common.parallelizer import (
+    printout,
+    parallel_warn,
+    get_rank,
+    get_comm,
+)
 from mala.targets.calculation_helpers import fermi_function
 from mala.common.physical_data import PhysicalData
 from mala.descriptors.atomic_density import AtomicDensity
@@ -1333,6 +1339,8 @@ def write_tem_input_file(
         qe_pseudopotentials,
         grid_dimensions,
         kpoints,
+        mpi_communicator,
+        mpi_rank,
     ):
         """
         Write a QE-style input file for the total energy module.
@@ -1360,6 +1368,14 @@ def write_tem_input_file(
 
         kpoints : dict
             k-grid used, usually None or (1,1,1) for TEM calculations.
+
+        mpi_communicator : MPI.COMM_WORLD
+            An MPI comminucator. If no MPI is enabled, this will simply be
+            None.
+
+        mpi_rank : int
+            Rank within MPI
+
         """
         # Specify grid dimensions, if any are given.
         if (
@@ -1379,14 +1395,24 @@ def write_tem_input_file(
         # the DFT calculation. If symmetry is then on in here, that
         # leads to errors.
         # qe_input_data["nosym"] = False
+        if mpi_rank == 0:
+            tem_input_file = tempfile.NamedTemporaryFile(
+                delete=False, prefix="mala.pw.scf.", suffix=".in", dir="./"
+            ).name
+        else:
+            tem_input_file = None
+
+        if mpi_communicator is not None:
+            tem_input_file = mpi_communicator.bcast(tem_input_file, root=0)
         ase.io.write(
-            "mala.pw.scf.in",
+            tem_input_file,
             atoms_Angstrom,
             "espresso-in",
             input_data=qe_input_data,
             pseudopotentials=qe_pseudopotentials,
             kpts=kpoints,
         )
+        return tem_input_file
 
     def restrict_data(self, array):
         """