Merged collection of updates for the latest aiida, aiida-vasp, and ph…

…onopy

.gitignore

@@ -0,0 +1,42 @@
+*.py[cod]
+*~
+MANIFEST
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Doc
+.buildinfo
+.doctrees
+_build

README.md

@@ -1,20 +1,6 @@
-
 AiiDA Phonopy plugin
 ====================
 
-This a phonopy plugin for AiiDA. This plugin includes workflows to calculate
-phonon band structure, DOS, thermal properties and mode Gruneisen parameters.
-It provides interfaces for VASP, Quantum ESPRESSO and LAMMPS to calculate the 
-atomic forces and relax the crystal structure. 
-
-
-Examples
---------
-Some test calculations are found in the folder **/examples**
-
-- plugins: examples of basic functionality of phonopy remote plugin. These tests require 
-the previous calculation of forces or force constants that should be already stored in the database
-- workchains: examples of the full phonon calculation / gruneisen parameters from scratch. These workflows
-require the installation of plugins for VASP, LAMMPS or QuantumESPRESSO.
-- tools: example scripts for visualize the results of phonon/gruneisen workchains. These scripts require
- matplotlib.
+This a phonopy plugin for AiiDA. This plugin includes workflows to
+calculate phonons with supercell and finite displacement approaches.
+Currently it provides interfaces only to VASP.

aiida_phonopy/calcs/base.py

@@ -0,0 +1,120 @@
+from aiida.common import CalcInfo, CodeInfo
+from aiida.plugins import DataFactory
+from aiida_phonopy.common.raw_parsers import (get_BORN_txt,
+                                              get_phonopy_conf_file_txt,
+                                              get_poscar_txt)
+
+Dict = DataFactory('dict')
+StructureData = DataFactory('structure')
+ArrayData = DataFactory('array')
+
+
+class BasePhonopyCalculation(object):
+    """
+    A basic plugin for calculating force constants using Phonopy.
+    Requirement: the node should be able to import phonopy if NAC is used
+    """
+
+    _INPUT_CELL = 'POSCAR'
+    _INPUT_FORCE_SETS = 'FORCE_SETS'
+    _INPUT_NAC = 'BORN'
+
+    @classmethod
+    def _baseclass_use_methods(cls, spec):
+        spec.input('settings', valid_type=Dict, required=True,
+                   help=('Use a node that specifies the phonopy '
+                         'parameters for the namelists'))
+        spec.input('structure', valid_type=StructureData, required=True,
+                   help=('Use a node for the structure'))
+        spec.input('force_sets', valid_type=ArrayData, required=False,
+                   help=('Use a node that specifies the force_sets '
+                         'array for the namelists'))
+        spec.input('nac_params', valid_type=ArrayData, required=False,
+                   help=('Use a node for the Non-analitical '
+                         'corrections parameters arrays'))
+        spec.input('primitive', valid_type=StructureData,
+                   required=False, help=('Use a node for the structure'))
+        spec.input('metadata.options.withmpi', valid_type=bool, default=False)
+
+    def _create_additional_files(self, folder):
+        pass
+
+    def prepare_for_submission(self, folder):
+        """Create the input files from the input nodes passed to this instance of the `CalcJob`.
+
+        :param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
+        :return: `aiida.common.datastructures.CalcInfo` instance
+        """
+
+        self.logger.info("prepare_for_submission")
+
+        self._internal_retrieve_list = []
+        self._additional_cmd_params = []
+        self._calculation_cmd = []
+
+        settings = self.inputs.settings
+        structure = self.inputs.structure
+        code = self.inputs.code
+
+        ##############################
+        # END OF INITIAL INPUT CHECK #
+        ##############################
+
+        # ================= prepare the python input files =================
+
+        self._create_additional_files(folder)
+
+        cell_txt = get_poscar_txt(structure)
+        input_txt = get_phonopy_conf_file_txt(settings)
+
+        input_filename = folder.get_abs_path(
+            self.inputs.metadata.options.input_filename)
+        with open(input_filename, 'w') as infile:
+            infile.write(input_txt)
+
+        cell_filename = folder.get_abs_path(self._INPUT_CELL)
+        with open(cell_filename, 'w') as infile:
+            infile.write(cell_txt)
+
+        if ('nac_params' in self.inputs and
+            'primitive' in self.inputs):
+            born_txt = get_BORN_txt(
+                self.inputs.nac_params,
+                self.inputs.primitive,
+                settings['symmetry_tolerance'])
+
+            nac_filename = folder.get_abs_path(self._INPUT_NAC)
+            with open(nac_filename, 'w') as infile:
+                infile.write(born_txt)
+            for params in self._additional_cmd_params:
+                params.append('--nac')
+
+        # ============================ calcinfo ===============================
+
+        local_copy_list = []
+        remote_copy_list = []
+
+        calcinfo = CalcInfo()
+
+        calcinfo.uuid = self.uuid
+
+        # Empty command line by default
+        calcinfo.local_copy_list = local_copy_list
+        calcinfo.remote_copy_list = remote_copy_list
+
+        # Retrieve files
+        calcinfo.retrieve_list = self._internal_retrieve_list
+
+        calcinfo.codes_info = []
+        for default_params, additional_params in zip(
+                self._calculation_cmd, self._additional_cmd_params):
+            codeinfo = CodeInfo()
+            codeinfo.cmdline_params = (
+                [self.inputs.metadata.options.input_filename, ]
+                + default_params + additional_params)
+            codeinfo.code_uuid = code.uuid
+            codeinfo.stdout_name = self.inputs.metadata.options.output_filename
+            codeinfo.withmpi = False
+            calcinfo.codes_info.append(codeinfo)
+
+        return calcinfo

aiida_phonopy/calculations/phonopy/phono3py.py → aiida_phonopy/calcs/phono3py.py

@@ -1,12 +1,12 @@
-from aiida.common.exceptions import InputValidationError
-from aiida.orm.calculation.job import JobCalculation
+from aiida.common import InputValidationError
+from aiida.engine import CalcJob
 from aiida.common.utils import classproperty
-from aiida.orm import DataFactory
-from aiida_phonopy.calculations.phonopy import BasePhonopyCalculation
-
-
-from aiida_phonopy.common.raw_parsers import get_disp_fc3_txt, get_forces_txt, \
-    write_fc2_to_hdf5_file, write_fc3_to_hdf5_file, write_kappa_to_hdf5_file
+from aiida.plugins import DataFactory
+from aiida_phonopy.calcs.base import BasePhonopyCalculation
+from aiida_phonopy.common.raw_parsers import (get_disp_fc3_txt, get_forces_txt,
+                                              write_fc2_to_hdf5_file,
+                                              write_fc3_to_hdf5_file,
+                                              write_kappa_to_hdf5_file)
 
 BandStructureData = DataFactory('phonopy.band_structure')
 KpointsData = DataFactory('array.kpoints')
@@ -28,7 +28,8 @@ def get_grid_data_files(grid_data):
 
     return gp_data
 
-class Phono3pyCalculation(BasePhonopyCalculation, JobCalculation):
+
+class Phono3pyCalculation(BasePhonopyCalculation, CalcJob):
     """
     A basic plugin for calculating phonon properties using Phonopy.
     """
@@ -64,14 +65,15 @@ def _use_methods(cls):
             'valid_types': ArrayData,
             'additional_parameter': None,
             'linkname': 'grid_data',
-            'docstring': "Use the node to include grid points data in distributed calculation",
+            'docstring': ("Use the node to include grid points data in "
+                          "distributed calculation"),
         }
 
         return retdict
 
     def _create_additional_files(self, tempfolder, inputdict):
 
-        data_sets = inputdict.pop(self.get_linkname('data_sets'), None)
+        datasets = inputdict.pop(self.get_linkname('datasets'), None)
         fc3 = inputdict.pop(self.get_linkname('force_constants_3'), None)
         fc2 = inputdict.pop(self.get_linkname('force_constants'), None)
 
@@ -90,18 +92,21 @@ def _create_additional_files(self, tempfolder, inputdict):
 
             self._additional_cmdline_params += ['--fc2', '--fc3']
 
-        elif data_sets is not None:
+        elif datasets is not None:
             disp_fc3_filename = tempfolder.get_abs_path(self._INPUT_DISP_FC3)
-            disp_f3c_txt = get_disp_fc3_txt(structure, parameters_data, data_sets)
+            disp_f3c_txt = get_disp_fc3_txt(
+                structure, parameters_data, datasets)
             with open(disp_fc3_filename, 'w') as infile:
                 infile.write(disp_f3c_txt)
 
-            forces_txt = get_forces_txt(data_sets)
+            forces_txt = get_forces_txt(datasets)
             forces_filename = tempfolder.get_abs_path(self._INPUT_FORCES_FC3)
             with open(forces_filename, 'w') as infile:
                 infile.write(forces_txt)
         else:
-            raise InputValidationError("either force_sets or force_constants should be specified for this calculation")
+            msg = ("either force_sets or force_constants should be specified "
+                   "for this calculation")
+            raise InputValidationError(msg)
 
         grid_data = inputdict.pop(self.get_linkname('grid_data'), None)
 
@@ -111,21 +116,26 @@ def _create_additional_files(self, tempfolder, inputdict):
                 kappa_g_filename = self._OUTPUT_KAPPA + \
                                'm{}{}{}'.format(*parameters_data.dict.mesh) + \
                                '-g{}.hdf5'.format(gp)
-                write_kappa_to_hdf5_file(gp_data[gp],
-                                         filename=tempfolder.get_abs_path(kappa_g_filename))
+                write_kappa_to_hdf5_file(
+                    gp_data[gp],
+                    filename=tempfolder.get_abs_path(kappa_g_filename))
 
             self._additional_cmdline_params += ['--read-gamma']
         else:
             if 'grid_point' in parameters_data.get_dict():
-                gp_string = ','.join([str(gp) for gp in parameters_data.dict.grid_point])
-                self._additional_cmdline_params += ['--gp={}'.format(gp_string), '--write-gamma']
+                gp_string = ','.join(
+                    [str(gp) for gp in parameters_data.dict.grid_point])
+                self._additional_cmdline_params += [
+                    '--gp={}'.format(gp_string), '--write-gamma']
                 for gp in parameters_data.dict.grid_point:
-                    kappa_g_filename = self._OUTPUT_KAPPA + \
-                                       'm{}{}{}'.format(*parameters_data.dict.mesh) + \
-                                       '-g{}.hdf5'.format(gp)
+                    kappa_g_filename = (
+                        self._OUTPUT_KAPPA +
+                        'm{}{}{}'.format(*parameters_data.dict.mesh) +
+                        '-g{}.hdf5'.format(gp))
                     self._internal_retrieve_list += [kappa_g_filename]
                 return
 
         # Set name for output file
-        kappa_filename = self._OUTPUT_KAPPA + 'm{}{}{}.hdf5'.format(*parameters_data.dict.mesh)
+        kappa_filename = (self._OUTPUT_KAPPA +
+                          'm{}{}{}.hdf5'.format(*parameters_data.dict.mesh))
         self._internal_retrieve_list += [kappa_filename]