Adding tests to check the override of structural paramters handling t…

…he boundary and dimensionality of the structure.
JPchico · Apr 25, 2024 · 4288e07 · 4288e07
1 parent 1416d37
commit 4288e07
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Showing 4 changed files with 178 additions and 7 deletions.
diff --git a/conftest.py b/conftest.py
@@ -1,6 +1,7 @@
 """
 initialise a test database and profile
 """
+
 # pylint: disable=redefined-outer-name
 from __future__ import annotations
 
@@ -13,7 +14,7 @@
 
 from aiida import orm
 from aiida.common import AttributeDict, CalcInfo, LinkType, exceptions
-from aiida.engine import CalcJob
+from aiida.engine import CalcJob, Process
 from aiida.engine.utils import instantiate_process
 from aiida.manage.manager import get_manager
 from aiida.plugins import WorkflowFactory
@@ -67,6 +68,12 @@ def pytest_report_header(config):
     ]
 
 
+@pytest.fixture
+def structure_parameters() -> AttributeDict:
+    parameteters = AttributeDict({"dimension": 2, "boundary": ["p", "p", "f"]})
+    return parameteters
+
+
 @pytest.fixture
 def filepath_tests() -> pathlib.Path:
     """Return the path to the tests folder."""
@@ -567,7 +574,7 @@ def factory(
         entry_point_name: str,
         inputs: dict[str, Any] | None = None,
         return_process: bool = False,
-    ) -> tuple[pathlib.Path, CalcInfo] | CalcJob:
+    ) -> tuple[pathlib.Path, CalcInfo] | Process:
         """Create a :class:`aiida.engine.CalcJob` instance with the given inputs.
 
         :param entry_point_name: The entry point name of the calculation job plugin to run.

diff --git a/tests/test_generate_inputs.py b/tests/test_generate_inputs.py
@@ -1,4 +1,5 @@
 """Functions to tests the input file generation"""
+
 import os
 
 import pytest
@@ -20,32 +21,39 @@ def validate_input_parameters(parameters: dict):
 
 
 @pytest.mark.parametrize(
-    "potential_type",
-    ["eam_alloy"],
+    "potential_type,override_parameters",
+    [("eam_alloy", True), ("eam_alloy", False)],
 )
 def test_input_generate_minimize(
     db_test_app,  # pylint: disable=unused-argument
     parameters_minimize,
     get_lammps_potential_data,
+    structure_parameters,
     potential_type,
+    override_parameters,
     file_regression,
 ):
     """Test the generation of the input file for minimize calculations"""
     # pylint: disable=too-many-locals
-
-    validate_input_parameters(parameters_minimize)
+    if override_parameters:
+        _parameters = parameters_minimize
+        _parameters["structure"].update(structure_parameters)
+    else:
+        _parameters = parameters_minimize
+    validate_input_parameters(_parameters)
     # Generate the potential
     potential_information = get_lammps_potential_data(potential_type)
     potential = LammpsPotentialData.get_or_create(
         source=potential_information["filename"],
         filename=potential_information["filename"],
         **potential_information["parameters"],
     )
+
     # Generating the structure
     structure = potential_information["structure"]
     # Generating the input file
     input_file = inputfile.generate_input_file(
-        parameters=parameters_minimize,
+        parameters=_parameters,
         potential=potential,
         structure=structure,
         trajectory_filename="temp.dump",

diff --git a/tests/test_generate_inputs/test_input_generate_minimize_eam_alloy_False_.txt b/tests/test_generate_inputs/test_input_generate_minimize_eam_alloy_False_.txt
@@ -0,0 +1,78 @@
+#------------------------Start of the Control information------------------------#
+clear
+units metal
+newton on
+timestep 1e-05
+#-------------------------End of the Control information-------------------------#
+#-----------------------Start of the Structure information-----------------------#
+box tilt small
+dimension 3
+boundary p p p 
+atom_style atomic
+read_data structure.dat
+#------------------------End of the Structure information------------------------#
+#-------------------------Start of Potential information-------------------------#
+pair_style eam/alloy 
+pair_coeff * * potential.dat Fe Fe
+#--------------------------End of Potential information--------------------------#
+#--------------------------Start of the Fix information--------------------------#
+fix box_relax_all_aiida all box/relax iso 0.0 vmax 0.001
+#---------------------------End of the Fix information---------------------------#
+#------------------------Start of the Compute information------------------------#
+compute pe_atom_all_aiida all pe/atom    
+compute ke_atom_all_aiida all ke/atom    
+compute stress_atom_all_aiida all stress/atom NULL
+compute pressure_all_aiida all pressure thermo_temp
+#-------------------------End of the Compute information-------------------------#
+#------------------------Start of the Thermo information-------------------------#
+thermo_style custom step pe ke press pxx pyy pzz etotal c_pressure_all_aiida c_pressure_all_aiida[1] c_pressure_all_aiida[2] c_pressure_all_aiida[3] c_pressure_all_aiida[4] c_pressure_all_aiida[5] c_pressure_all_aiida[6]
+thermo 100
+#-------------------------End of the Thermo information--------------------------#
+#-------------------------Start of the Dump information--------------------------#
+dump aiida all custom 1000 temp.dump id type element x y z c_pe_atom_all_aiida c_ke_atom_all_aiida c_stress_atom_all_aiida[1] c_stress_atom_all_aiida[2] c_stress_atom_all_aiida[3] c_stress_atom_all_aiida[4] c_stress_atom_all_aiida[5] c_stress_atom_all_aiida[6]
+dump_modify aiida sort id
+dump_modify aiida element Fe Fe
+dump_modify aiida format line "%6d %4d %4s %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f"
+#--------------------------End of the Dump information---------------------------#
+#---------------------Start of the Minimization information----------------------#
+min_style cg
+minimize 1e-05 1e-05 5000 5000
+#----------------------End of the Minimization information-----------------------#
+#--------------------Start of the Final Variables information--------------------#
+variable final_step equal step
+variable final_pe equal pe
+variable final_ke equal ke
+variable final_press equal press
+variable final_pxx equal pxx
+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]
+#---------------------End of the Final Variables information---------------------#
+#---------------Start of the Printing Final Variables information----------------#
+print "#Final results" file aiida_lammps.yaml
+print "final_step: ${final_step}" append aiida_lammps.yaml
+print "final_pe: ${final_pe}" append aiida_lammps.yaml
+print "final_ke: ${final_ke}" append aiida_lammps.yaml
+print "final_press: ${final_press}" append aiida_lammps.yaml
+print "final_pxx: ${final_pxx}" append aiida_lammps.yaml
+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
+#----------------End of the Printing Final Variables information-----------------#
+#---------------------Start of the write restart information---------------------#
+write_restart restart.aiida
+#----------------------End of the write restart information----------------------#
diff --git a/tests/test_generate_inputs/test_input_generate_minimize_eam_alloy_True_.txt b/tests/test_generate_inputs/test_input_generate_minimize_eam_alloy_True_.txt
@@ -0,0 +1,78 @@
+#------------------------Start of the Control information------------------------#
+clear
+units metal
+newton on
+timestep 1e-05
+#-------------------------End of the Control information-------------------------#
+#-----------------------Start of the Structure information-----------------------#
+box tilt small
+dimension 2
+boundary p p f 
+atom_style atomic
+read_data structure.dat
+#------------------------End of the Structure information------------------------#
+#-------------------------Start of Potential information-------------------------#
+pair_style eam/alloy 
+pair_coeff * * potential.dat Fe Fe
+#--------------------------End of Potential information--------------------------#
+#--------------------------Start of the Fix information--------------------------#
+fix box_relax_all_aiida all box/relax iso 0.0 vmax 0.001
+#---------------------------End of the Fix information---------------------------#
+#------------------------Start of the Compute information------------------------#
+compute pe_atom_all_aiida all pe/atom    
+compute ke_atom_all_aiida all ke/atom    
+compute stress_atom_all_aiida all stress/atom NULL
+compute pressure_all_aiida all pressure thermo_temp
+#-------------------------End of the Compute information-------------------------#
+#------------------------Start of the Thermo information-------------------------#
+thermo_style custom step pe ke press pxx pyy pzz etotal c_pressure_all_aiida c_pressure_all_aiida[1] c_pressure_all_aiida[2] c_pressure_all_aiida[3] c_pressure_all_aiida[4] c_pressure_all_aiida[5] c_pressure_all_aiida[6]
+thermo 100
+#-------------------------End of the Thermo information--------------------------#
+#-------------------------Start of the Dump information--------------------------#
+dump aiida all custom 1000 temp.dump id type element x y z c_pe_atom_all_aiida c_ke_atom_all_aiida c_stress_atom_all_aiida[1] c_stress_atom_all_aiida[2] c_stress_atom_all_aiida[3] c_stress_atom_all_aiida[4] c_stress_atom_all_aiida[5] c_stress_atom_all_aiida[6]
+dump_modify aiida sort id
+dump_modify aiida element Fe Fe
+dump_modify aiida format line "%6d %4d %4s %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f %16.10f"
+#--------------------------End of the Dump information---------------------------#
+#---------------------Start of the Minimization information----------------------#
+min_style cg
+minimize 1e-05 1e-05 5000 5000
+#----------------------End of the Minimization information-----------------------#
+#--------------------Start of the Final Variables information--------------------#
+variable final_step equal step
+variable final_pe equal pe
+variable final_ke equal ke
+variable final_press equal press
+variable final_pxx equal pxx
+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]
+#---------------------End of the Final Variables information---------------------#
+#---------------Start of the Printing Final Variables information----------------#
+print "#Final results" file aiida_lammps.yaml
+print "final_step: ${final_step}" append aiida_lammps.yaml
+print "final_pe: ${final_pe}" append aiida_lammps.yaml
+print "final_ke: ${final_ke}" append aiida_lammps.yaml
+print "final_press: ${final_press}" append aiida_lammps.yaml
+print "final_pxx: ${final_pxx}" append aiida_lammps.yaml
+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
+#----------------End of the Printing Final Variables information-----------------#
+#---------------------Start of the write restart information---------------------#
+write_restart restart.aiida
+#----------------------End of the write restart information----------------------#