Merge pull request #563 from timcallow/lammps_tempfile

Use tempfile module for lammps file generation

mala/descriptors/atomic_density.py

@@ -137,9 +137,8 @@ def __calculate_lammps(self, outdir, **kwargs):
  keep_logs = kwargs.get("keep_logs", False)
 
  lammps_format = "lammps-data"
- self.lammps_temporary_input = os.path.join(
- outdir, "lammps_input_" + self.calculation_timestamp + ".tmp"
- )
+ self.setup_lammps_tmp_files("ggrid", outdir)
+
  ase.io.write(
  self.lammps_temporary_input, self.atoms, format=lammps_format
  )
@@ -160,10 +159,6 @@ def __calculate_lammps(self, outdir, **kwargs):
  "sigma": self.parameters.atomic_density_sigma,
  "rcutfac": self.parameters.atomic_density_cutoff,
  }
- self.lammps_temporary_log = os.path.join(
- outdir,
- "lammps_ggrid_log_" + self.calculation_timestamp + ".tmp",
- )
  lmp = self._setup_lammps(nx, ny, nz, lammps_dict)
 
  # For now the file is chosen automatically, because this is used

mala/descriptors/bispectrum.py

@@ -1,6 +1,7 @@
 """Bispectrum descriptor class."""
 
 import os
+import tempfile
 
 import ase
 import ase.io
@@ -141,9 +142,8 @@ def __calculate_lammps(self, outdir, **kwargs):
  keep_logs = kwargs.get("keep_logs", False)
 
  lammps_format = "lammps-data"
- self.lammps_temporary_input = os.path.join(
- outdir, "lammps_input_" + self.calculation_timestamp + ".tmp"
- )
+ self.setup_lammps_tmp_files("bgrid", outdir)
+
  ase.io.write(
  self.lammps_temporary_input, self.atoms, format=lammps_format
  )
@@ -157,11 +157,6 @@ def __calculate_lammps(self, outdir, **kwargs):
  "twojmax": self.parameters.bispectrum_twojmax,
  "rcutfac": self.parameters.bispectrum_cutoff,
  }
-
- self.lammps_temporary_log = os.path.join(
- outdir,
- "lammps_bgrid_log_" + self.calculation_timestamp + ".tmp",
- )
  lmp = self._setup_lammps(nx, ny, nz, lammps_dict)
 
  # An empty string means that the user wants to use the standard input.
@@ -227,6 +222,7 @@ def __calculate_lammps(self, outdir, **kwargs):
  array_shape=(nrows_local, ncols_local),
  use_fp64=use_fp64,
  )
+
  self._clean_calculation(lmp, keep_logs)
 
  # Copy the grid dimensions only at the end.
@@ -243,6 +239,7 @@ def __calculate_lammps(self, outdir, **kwargs):
  (nz, ny, nx, self.fingerprint_length),
  use_fp64=use_fp64,
  )
+
  self._clean_calculation(lmp, keep_logs)
 
  # switch from x-fastest to z-fastest order (swaps 0th and 2nd
@@ -511,7 +508,6 @@ def __calculate_python(self, **kwargs):
  ########
 
  class _ZIndices:
-
  def __init__(self):
  self.j1 = 0
  self.j2 = 0
@@ -525,7 +521,6 @@ def __init__(self):
  self.jju = 0
 
  class _BIndices:
-
  def __init__(self):
  self.j1 = 0
  self.j2 = 0
@@ -968,21 +963,21 @@ 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

@@ -1,9 +1,9 @@
 """Base class for all descriptor calculators."""
 
 from abc import abstractmethod
-from datetime import datetime
 from functools import cached_property
 import os
+import tempfile
 
 import ase
 from ase.units import m
@@ -163,26 +163,6 @@ def descriptors_contain_xyz(self):
  def descriptors_contain_xyz(self, value):
  self.parameters.descriptors_contain_xyz = value
 
- @cached_property
- def calculation_timestamp(self):
- """
- Timestamp of calculation start.
-
- Used to distinguish multiple LAMMPS runs performed in the same
- directory. Since the interface is file based, this timestamp prevents
- problems with slightly
- """
- if get_rank() == 0:
- timestamp = datetime.timestamp(datetime.utcnow())
- else:
- timestamp = None
-
- if self.parameters._configuration["mpi"]:
- timestamp = get_comm().bcast(timestamp, root=0)
- return datetime.fromtimestamp(timestamp).strftime("%F-%H-%M-%S-%f")[
- :-3
- ]
-
  ##############################
  # Methods
  ##############################
@@ -238,6 +218,44 @@ def backconvert_units(array, out_units):
  "this descriptor type."
  )
 
+ def setup_lammps_tmp_files(self, lammps_type, outdir):
+ """
+ Create the temporary lammps input and log files.
+
+ Parameters
+ ----------
+ lammps_type: str
+ 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(
+ 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(
+ 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
+
+ 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)
+
+
  # Calculations
  ##############
 
@@ -827,10 +845,6 @@ def _clean_calculation(self, lmp, keep_logs):
  os.remove(self.lammps_temporary_log)
  os.remove(self.lammps_temporary_input)
 
- # Reset timestamp for potential next calculation using same LAMMPS
- # object.
- del self.calculation_timestamp
-
  def _setup_atom_list(self):
  """
  Set up a list of atoms potentially relevant for descriptor calculation.

mala/descriptors/minterpy_descriptors.py

@@ -163,9 +163,8 @@ def _calculate(self, atoms, outdir, grid_dimensions, **kwargs):
 
  # The rest is the stanfard LAMMPS atomic density stuff.
  lammps_format = "lammps-data"
- self.lammps_temporary_input = os.path.join(
- outdir, "lammps_input_" + self.calculation_timestamp + ".tmp"
- )
+ self.setup_lammps_tmp_files("minterpy", outdir)
+
  ase.io.write(
  self.lammps_temporary_input, self.atoms, format=lammps_format
  )
@@ -175,10 +174,6 @@ def _calculate(self, atoms, outdir, grid_dimensions, **kwargs):
  "sigma": self.parameters.atomic_density_sigma,
  "rcutfac": self.parameters.atomic_density_cutoff,
  }
- self.lammps_temporary_log = os.path.join(
- outdir,
- "lammps_bgrid_log_" + self.calculation_timestamp + ".tmp",
- )
  lmp = self._setup_lammps(nx, ny, nz, lammps_dict)
 
  # For now the file is chosen automatically, because this is used