Merge pull request #43 from JPchico/workchains

Fixing an issue in which the arrays names do not conform to aiida's standards

aiida_lammps/calculations/lammps/base.py

@@ -31,7 +31,7 @@ class BaseLammpsCalculation(CalcJob):
 
     _DEFAULT_LOGFILE_FILENAME = "log.lammps"
     _DEFAULT_OUTPUT_FILENAME = "lammps_output"
-    _DEFAULT_TRAJECTORY_FILENAME = "aiida_lampps.trajectory.dump"
+    _DEFAULT_TRAJECTORY_FILENAME = "aiida_lammps.trajectory.dump"
     _DEFAULT_VARIABLES_FILENAME = "aiida_lammps.yaml"
     _DEFAULT_RESTART_FILENAME = "lammps.restart"
     _DEFAULT_POTENTIAL_FILENAME = "potential.dat"

aiida_lammps/common/generate_structure.py

@@ -52,11 +52,11 @@ def generate_lammps_structure(
 
     :param structure: the structure to use in the simulation
     :type structure: orm.StructureData
-    :param atom_style: treatment of the particles accroding to lammps, defaults to 'atomic'
+    :param atom_style: treatment of the particles according to lammps, defaults to 'atomic'
     :type atom_style: str, optional
     :param charge_dict: dictionary with the charge for the particles, defaults to None
     :type charge_dict: dict, optional
-    :param round_dp: precision to which to round the postions, defaults to None
+    :param round_dp: precision to which to round the positions, defaults to None
     :type round_dp: float, optional
     :param docstring: header for the structure file, defaults to 'generated by aiida_lammps'
     :type docstring: str, optional

aiida_lammps/common/input_generator.py

@@ -13,6 +13,7 @@
 from builtins import ValueError
 import json
 import os
+import re
 from typing import Union
 
 from aiida import orm
@@ -437,7 +438,7 @@ def write_final_variables_block(
     variables_block = generate_header("Start of the Final Variables information")
 
     for _thermo in fixed_thermo:
-        _variables.append(_thermo.replace("[", "_").replace("]", ""))
+        _variables.append(re.sub("[^a-zA-Z0-9_]", "__", _thermo))
         variables_block += f"variable final_{_variables[-1]} equal {_thermo}\n"
     variables_block += generate_header("End of the Final Variables information")
 

aiida_lammps/common/parse_trajectory.py

@@ -2,6 +2,7 @@
 """
 # pylint: disable=fixme
 from collections import namedtuple
+import re
 
 from aiida import orm
 import numpy as np
@@ -88,7 +89,9 @@ def parse_step(lines, initial_line=0) -> namedtuple:
         ]
     )
     cell = super_cell.T
-    field_names = lines[8].split()[2:]
+    field_names = [
+        re.sub("[^a-zA-Z0-9_]", "__", entry) for entry in lines[8].split()[2:]
+    ]
     fields = []
     for i in range(number_of_atoms):
         fields.append(lines[9 + i].split())

aiida_lammps/common/raw_parsers.py

@@ -80,7 +80,9 @@ def parse_logfile(filename: str = None, file_contents: str = None) -> Union[dict
             global_parsed_data["bin"] = line.split()[-1]
         if line.startswith("Step"):
             header_line_position = index
-            header_line = line.split()
+            header_line = [
+                re.sub("[^a-zA-Z0-9_]", "__", entry) for entry in line.split()
+            ]
         if header_line_position > 0 and index != header_line_position and not end_found:
             if not line.split()[0].replace(".", "", 1).isdigit():
                 end_found = True

tests/test_calculations/test_optimize_process_eam_.yml

@@ -31,12 +31,12 @@ trajectory_data:
   elements:
   - Fe
   field_names:
-  - c_stpa[1]
-  - c_stpa[2]
-  - c_stpa[3]
-  - c_stpa[4]
-  - c_stpa[5]
-  - c_stpa[6]
+  - c_stpa__1__
+  - c_stpa__2__
+  - c_stpa__3__
+  - c_stpa__4__
+  - c_stpa__5__
+  - c_stpa__6__
   - element
   - fx
   - fy

tests/test_calculations/test_optimize_process_lennard_jones_.yml

@@ -30,12 +30,12 @@ trajectory_data:
   elements:
   - Ar
   field_names:
-  - c_stpa[1]
-  - c_stpa[2]
-  - c_stpa[3]
-  - c_stpa[4]
-  - c_stpa[5]
-  - c_stpa[6]
+  - c_stpa__1__
+  - c_stpa__2__
+  - c_stpa__3__
+  - c_stpa__4__
+  - c_stpa__5__
+  - c_stpa__6__
   - element
   - fx
   - fy

tests/test_calculations/test_optimize_process_reaxff_.yml

@@ -33,12 +33,12 @@ trajectory_data:
   - Fe
   - S
   field_names:
-  - c_stpa[1]
-  - c_stpa[2]
-  - c_stpa[3]
-  - c_stpa[4]
-  - c_stpa[5]
-  - c_stpa[6]
+  - c_stpa__1__
+  - c_stpa__2__
+  - c_stpa__3__
+  - c_stpa__4__
+  - c_stpa__5__
+  - c_stpa__6__
   - element
   - fx
   - fy

tests/test_calculations/test_optimize_process_tersoff_.yml

@@ -32,12 +32,12 @@ trajectory_data:
   - Ga
   - N
   field_names:
-  - c_stpa[1]
-  - c_stpa[2]
-  - c_stpa[3]
-  - c_stpa[4]
-  - c_stpa[5]
-  - c_stpa[6]
+  - c_stpa__1__
+  - c_stpa__2__
+  - c_stpa__3__
+  - c_stpa__4__
+  - c_stpa__5__
+  - c_stpa__6__
   - element
   - fx
   - fy

tests/test_generate_inputs/test_generate_input_eam_alloy_md.txt

@@ -50,12 +50,12 @@ variable final_pyy equal pyy
 variable final_pzz equal pzz
 variable final_etotal equal etotal
 variable final_c_pressure_all_aiida equal c_pressure_all_aiida
-variable final_c_pressure_all_aiida_1 equal c_pressure_all_aiida[1]
-variable final_c_pressure_all_aiida_2 equal c_pressure_all_aiida[2]
-variable final_c_pressure_all_aiida_3 equal c_pressure_all_aiida[3]
-variable final_c_pressure_all_aiida_4 equal c_pressure_all_aiida[4]
-variable final_c_pressure_all_aiida_5 equal c_pressure_all_aiida[5]
-variable final_c_pressure_all_aiida_6 equal c_pressure_all_aiida[6]
+variable final_c_pressure_all_aiida__1__ equal c_pressure_all_aiida[1]
+variable final_c_pressure_all_aiida__2__ equal c_pressure_all_aiida[2]
+variable final_c_pressure_all_aiida__3__ equal c_pressure_all_aiida[3]
+variable final_c_pressure_all_aiida__4__ equal c_pressure_all_aiida[4]
+variable final_c_pressure_all_aiida__5__ equal c_pressure_all_aiida[5]
+variable final_c_pressure_all_aiida__6__ equal c_pressure_all_aiida[6]
 #---------------------End of the Final Variables information---------------------#
 #---------------Start of the Printing Final Variables information----------------#
 print "#Final results" file aiida_lammps.yaml
@@ -68,12 +68,12 @@ print "final_pyy: ${final_pyy}" append aiida_lammps.yaml
 print "final_pzz: ${final_pzz}" append aiida_lammps.yaml
 print "final_etotal: ${final_etotal}" append aiida_lammps.yaml
 print "final_c_pressure_all_aiida: ${final_c_pressure_all_aiida}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_1: ${final_c_pressure_all_aiida_1}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_2: ${final_c_pressure_all_aiida_2}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_3: ${final_c_pressure_all_aiida_3}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_4: ${final_c_pressure_all_aiida_4}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_5: ${final_c_pressure_all_aiida_5}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_6: ${final_c_pressure_all_aiida_6}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__1__: ${final_c_pressure_all_aiida__1__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__2__: ${final_c_pressure_all_aiida__2__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__3__: ${final_c_pressure_all_aiida__3__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__4__: ${final_c_pressure_all_aiida__4__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__5__: ${final_c_pressure_all_aiida__5__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__6__: ${final_c_pressure_all_aiida__6__}" append aiida_lammps.yaml
 #----------------End of the Printing Final Variables information-----------------#
 #---------------------Start of the write restart information---------------------#
 write_restart restart.aiida

tests/test_generate_inputs/test_generate_input_eam_alloy_minimize.txt

@@ -48,12 +48,12 @@ variable final_pyy equal pyy
 variable final_pzz equal pzz
 variable final_etotal equal etotal
 variable final_c_pressure_all_aiida equal c_pressure_all_aiida
-variable final_c_pressure_all_aiida_1 equal c_pressure_all_aiida[1]
-variable final_c_pressure_all_aiida_2 equal c_pressure_all_aiida[2]
-variable final_c_pressure_all_aiida_3 equal c_pressure_all_aiida[3]
-variable final_c_pressure_all_aiida_4 equal c_pressure_all_aiida[4]
-variable final_c_pressure_all_aiida_5 equal c_pressure_all_aiida[5]
-variable final_c_pressure_all_aiida_6 equal c_pressure_all_aiida[6]
+variable final_c_pressure_all_aiida__1__ equal c_pressure_all_aiida[1]
+variable final_c_pressure_all_aiida__2__ equal c_pressure_all_aiida[2]
+variable final_c_pressure_all_aiida__3__ equal c_pressure_all_aiida[3]
+variable final_c_pressure_all_aiida__4__ equal c_pressure_all_aiida[4]
+variable final_c_pressure_all_aiida__5__ equal c_pressure_all_aiida[5]
+variable final_c_pressure_all_aiida__6__ equal c_pressure_all_aiida[6]
 #---------------------End of the Final Variables information---------------------#
 #---------------Start of the Printing Final Variables information----------------#
 print "#Final results" file aiida_lammps.yaml
@@ -66,12 +66,12 @@ print "final_pyy: ${final_pyy}" append aiida_lammps.yaml
 print "final_pzz: ${final_pzz}" append aiida_lammps.yaml
 print "final_etotal: ${final_etotal}" append aiida_lammps.yaml
 print "final_c_pressure_all_aiida: ${final_c_pressure_all_aiida}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_1: ${final_c_pressure_all_aiida_1}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_2: ${final_c_pressure_all_aiida_2}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_3: ${final_c_pressure_all_aiida_3}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_4: ${final_c_pressure_all_aiida_4}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_5: ${final_c_pressure_all_aiida_5}" append aiida_lammps.yaml
-print "final_c_pressure_all_aiida_6: ${final_c_pressure_all_aiida_6}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__1__: ${final_c_pressure_all_aiida__1__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__2__: ${final_c_pressure_all_aiida__2__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__3__: ${final_c_pressure_all_aiida__3__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__4__: ${final_c_pressure_all_aiida__4__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__5__: ${final_c_pressure_all_aiida__5__}" append aiida_lammps.yaml
+print "final_c_pressure_all_aiida__6__: ${final_c_pressure_all_aiida__6__}" append aiida_lammps.yaml
 #----------------End of the Printing Final Variables information-----------------#
 #---------------------Start of the write restart information---------------------#
 write_restart restart.aiida

tests/test_raw_parsers/test_parse_log.yaml

@@ -480,7 +480,7 @@ time_dependent:
   - -60616.181
   - -60998.054
   - -61353.826
-  c_pressure_all_aiida[1]:
+  c_pressure_all_aiida__1__:
   - -65784.86
   - -65754.123
   - -65658.395
@@ -532,7 +532,7 @@ time_dependent:
   - -56496.14
   - -56926.184
   - -57340.453
-  c_pressure_all_aiida[2]:
+  c_pressure_all_aiida__2__:
   - -66151.806
   - -66129.949
   - -66064.381
@@ -584,7 +584,7 @@ time_dependent:
   - -63084.235
   - -63403.866
   - -63702.654
-  c_pressure_all_aiida[3]:
+  c_pressure_all_aiida__3__:
   - -65307.943
   - -65282.65
   - -65204.64
@@ -636,7 +636,7 @@ time_dependent:
   - -62268.168
   - -62664.111
   - -63018.371
-  c_pressure_all_aiida[4]:
+  c_pressure_all_aiida__4__:
   - -968.80346
   - -973.77775
   - -989.84677
@@ -688,7 +688,7 @@ time_dependent:
   - -1884.7159
   - -1744.5319
   - -1602.112
-  c_pressure_all_aiida[5]:
+  c_pressure_all_aiida__5__:
   - -1835.8858
   - -1846.5829
   - -1879.7798
@@ -740,7 +740,7 @@ time_dependent:
   - -4043.8155
   - -3741.0193
   - -3438.0051
-  c_pressure_all_aiida[6]:
+  c_pressure_all_aiida__6__:
   - -293.61095
   - -291.26981
   - -286.53978