Merge pull request #8 from chrisjsewell/test-force

replace `generate_LAMMPS_structure` function and add more tests

aiida_lammps/__init__.py

@@ -1 +1 @@
-__version__ = "0.2.0b3"
+__version__ = "0.3.0b3"

aiida_lammps/calculations/lammps/__init__.py

@@ -1,9 +1,9 @@
 from aiida.engine import CalcJob
-from aiida.common import InputValidationError
 from aiida.common import CalcInfo, CodeInfo
 from aiida.orm import StructureData, Dict
 from aiida.plugins import DataFactory
 from aiida_lammps.common.utils import convert_date_string
+from aiida_lammps.common.generate_structure import generate_lammps_structure
 from aiida_lammps.data.potential import EmpiricalPotential
 import six
 
@@ -38,9 +38,9 @@ def get_FORCE_CONSTANTS_txt(force_constants):
     fc_txt = "%4d\n" % (fc_shape[0])
     for i in range(fc_shape[0]):
         for j in range(fc_shape[1]):
-            fc_txt += "%4d%4d\n" % (i+1, j+1)
+            fc_txt += "%4d%4d\n" % (i + 1, j + 1)
             for vec in force_constants[i][j]:
-                fc_txt +=("%22.15f"*3 + "\n") % tuple(vec)
+                fc_txt += ("%22.15f" * 3 + "\n") % tuple(vec)
 
     return fc_txt
 
@@ -55,8 +55,8 @@ def structure_to_poscar(structure):
     cell = structure.cell
     for row in cell:
         poscar += '{0: 22.16f} {1: 22.16f} {2: 22.16f}\n'.format(*row)
-    poscar += ' '.join(np.unique([site.kind_name for site in structure.sites]))+'\n'
-    poscar += ' '.join(np.array(labels, dtype=str))+'\n'
+    poscar += ' '.join(np.unique([site.kind_name for site in structure.sites])) + '\n'
+    poscar += ' '.join(np.array(labels, dtype=str)) + '\n'
     poscar += 'Cartesian\n'
     for site in structure.sites:
         poscar += '{0: 22.16f} {1: 22.16f} {2: 22.16f}\n'.format(*site.position)
@@ -83,73 +83,11 @@ def parameters_to_input_file(parameters_object):
     return input_file
 
 
-def generate_LAMMPS_structure(structure, atom_style):
-    import numpy as np
-
-    types = [site.kind_name for site in structure.sites]
-
-    type_index_unique = np.unique(types, return_index=True)[1]
-    count_index_unique = np.diff(np.append(type_index_unique, [len(types)]))
-
-    atom_index = []
-    for i, index in enumerate(count_index_unique):
-        atom_index += [i for j in range(index)]
-
-    masses = [site.mass for site in structure.kinds]
-    positions = [site.position for site in structure.sites]
-
-    number_of_atoms = len(positions)
-
-    lammps_data_file = 'Generated using dynaphopy\n\n'
-    lammps_data_file += '{0} atoms\n\n'.format(number_of_atoms)
-    lammps_data_file += '{0} atom types\n\n'.format(len(masses))
-
-    cell = np.array(structure.cell)
-
-    a = np.linalg.norm(cell[0])
-    b = np.linalg.norm(cell[1])
-    c = np.linalg.norm(cell[2])
-
-    alpha = np.arccos(np.dot(cell[1], cell[2])/(c*b))
-    gamma = np.arccos(np.dot(cell[1], cell[0])/(a*b))
-    beta = np.arccos(np.dot(cell[2], cell[0])/(a*c))
-
-    xhi = a
-    xy = b * np.cos(gamma)
-    xz = c * np.cos(beta)
-    yhi = np.sqrt(pow(b,2)- pow(xy,2))
-    yz = (b*c*np.cos(alpha)-xy * xz)/yhi
-    zhi = np.sqrt(pow(c,2)-pow(xz,2)-pow(yz,2))
-
-    xhi = xhi + max(0,0, xy, xz, xy+xz)
-    yhi = yhi + max(0,0, yz)
-
-    lammps_data_file += '\n{0:20.10f} {1:20.10f} xlo xhi\n'.format(0, xhi)
-    lammps_data_file += '{0:20.10f} {1:20.10f} ylo yhi\n'.format(0, yhi)
-    lammps_data_file += '{0:20.10f} {1:20.10f} zlo zhi\n'.format(0, zhi)
-    lammps_data_file += '{0:20.10f} {1:20.10f} {2:20.10f} xy xz yz\n\n'.format(xy, xz, yz)
-
-    lammps_data_file += 'Masses\n\n'
-
-    for i, mass in enumerate(masses):
-        lammps_data_file += '{0} {1:20.10f} \n'.format(i+1, mass)
-
-    lammps_data_file += '\nAtoms\n\n'
-    for i, row in enumerate(positions):
-        if atom_style == 'charge':
-            # TODO variable initial charge
-            lammps_data_file += '{0} {1} 0.0 {2:20.10f} {3:20.10f} {4:20.10f}\n'.format(i+1, atom_index[i]+1, row[0],row[1],row[2])
-        else:
-            lammps_data_file += '{0} {1} {2:20.10f} {3:20.10f} {4:20.10f}\n'.format(i+1, atom_index[i]+1, row[0],row[1],row[2])
-
-    return lammps_data_file
-
-
 def generate_LAMMPS_potential(pair_style):
 
     potential_file = '# Potential file generated by aiida plugin (please check citation in the orignal file)\n'
     for key, value in pair_style.dict.data.iteritems():
-         potential_file += '{}    {}\n'.format(key, value)
+        potential_file += '{}    {}\n'.format(key, value)
 
     return potential_file
 
@@ -175,22 +113,28 @@ class BaseLammpsCalculation(CalcJob):
     def define(cls, spec):
         super(BaseLammpsCalculation, cls).define(spec)
         spec.input('structure', valid_type=StructureData, help='the structure')
-        spec.input('potential', valid_type=EmpiricalPotential, help='lammps potential')
-        spec.input('parameters', valid_type=Dict, help='the parameters', required=False, default=Dict())
-        spec.input('metadata.options.output_filename', valid_type=six.string_types, default=cls._OUTPUT_FILE_NAME)
+        spec.input('potential', valid_type=EmpiricalPotential,
+                   help='lammps potential')
+        spec.input('parameters', valid_type=Dict,
+                   help='the parameters', required=False)
+        spec.input('metadata.options.output_filename',
+                   valid_type=six.string_types, default=cls._OUTPUT_FILE_NAME)
 
-        spec.default_output_port = 'results'
         spec.output('results',
                     valid_type=DataFactory('dict'),
                     required=True,
                     help='the data extracted from the main output file')
+        spec.default_output_node = 'results'
 
         # TODO review aiidateam/aiida_core#2997, when closed, for exit code formalization
 
         # Unrecoverable errors: resources like the retrieved folder or its expected contents are missing
         spec.exit_code(
             200, 'ERROR_NO_RETRIEVED_FOLDER',
             message='The retrieved folder data node could not be accessed.')
+        spec.exit_code(
+            201, 'ERROR_NO_RETRIEVED_TEMP_FOLDER',
+            message='The retrieved temporary folder data node could not be accessed.')
         spec.exit_code(
             210, 'ERROR_OUTPUT_FILE_MISSING',
             message='the main output file was not found')
@@ -220,7 +164,6 @@ def prepare_extra_files(self, tempfolder, potential_object):
         return True
 
     def prepare_for_submission(self, tempfolder):
-
         """Create the input files from the input nodes passed to this instance of the `CalcJob`.
 
         :param tempfolder: an `aiida.common.folders.Folder` to temporarily write files on disk
@@ -231,14 +174,20 @@ def prepare_for_submission(self, tempfolder):
         potential_txt = self.inputs.potential.get_potential_file()
 
         # Setup structure
-        structure_txt = generate_LAMMPS_structure(self.inputs.structure,
+        structure_txt = generate_lammps_structure(self.inputs.structure,
                                                   self.inputs.potential.atom_style)
 
+        if "parameters" in self.inputs:
+            parameters = self.inputs.parameters
+        else:
+            parameters = Dict()
+
         # Check lammps version date in parameters
-        lammps_date = convert_date_string(self.inputs.parameters.get_dict().get("lammps_version", '11 Aug 2017'))
+        lammps_date = convert_date_string(
+            parameters.get_dict().get("lammps_version", '11 Aug 2017'))
 
         # Setup input parameters
-        input_txt = self._generate_input_function(self.inputs.parameters,
+        input_txt = self._generate_input_function(parameters,
                                                   self.inputs.potential,
                                                   self._INPUT_STRUCTURE,
                                                   self._OUTPUT_TRAJECTORY_FILE_NAME,
@@ -249,7 +198,7 @@ def prepare_for_submission(self, tempfolder):
         with open(input_filename, 'w') as infile:
             infile.write(input_txt)
 
-        self.validate_parameters(self.inputs.parameters, self.inputs.potential)
+        self.validate_parameters(parameters, self.inputs.potential)
 
         # prepare extra files if needed
         self.prepare_extra_files(tempfolder, self.inputs.potential)
@@ -261,7 +210,8 @@ def prepare_for_submission(self, tempfolder):
             infile.write(structure_txt)
 
         if potential_txt is not None:
-            potential_filename = tempfolder.get_abs_path(self.inputs.potential.potential_filename)
+            potential_filename = tempfolder.get_abs_path(
+                self.inputs.potential.potential_filename)
             with open(potential_filename, 'w') as infile:
                 infile.write(potential_txt)
 

aiida_lammps/calculations/lammps/force.py

@@ -1,3 +1,4 @@
+from aiida.plugins import DataFactory
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
 from aiida_lammps.common.utils import convert_date_string
 import six
@@ -53,6 +54,11 @@ def define(cls, spec):
 
         # spec.input('settings', valid_type=six.string_types, default='lammps.optimize')
 
+        spec.output('arrays',
+                    valid_type=DataFactory('array'),
+                    required=True,
+                    help='force data per step')
+
     def validate_parameters(self, param_data, potential_object):
         self._retrieve_list += [self._OUTPUT_TRAJECTORY_FILE_NAME]
         self._retrieve_temporary_list += []

aiida_lammps/calculations/lammps/md.py

@@ -111,6 +111,7 @@ def validate_parameters(self, param_data, potential_object):
             ))
 
         self._retrieve_list += []
-        self._retrieve_temporary_list += [self._OUTPUT_TRAJECTORY_FILE_NAME]
+        if self._OUTPUT_TRAJECTORY_FILE_NAME not in self._retrieve_temporary_list:
+            self._retrieve_temporary_list += [self._OUTPUT_TRAJECTORY_FILE_NAME]
 
         return True