Merge pull request #89 from pyiron/merge

Merge

.ci_support/environment.yml

@@ -6,9 +6,9 @@ dependencies:
   - coverage
   - codacy-coverage
   - matplotlib =3.3.4
-  - numpy =1.20
-  - pyiron_base =0.1.46
-  - pyiron_atomistics =0.2.3
+  - numpy =1.20.1
+  - pyiron_base =0.1.48
+  - pyiron_atomistics =0.2.4
   - scipy =1.6.0
   - seaborn =0.11.1
   - scikit-image =0.18.1

pyiron_contrib/__init__.py

@@ -34,6 +34,12 @@
 JOB_CLASS_DICT['Fenics'] = 'pyiron_contrib.continuum.fenics.job.generic'
 JOB_CLASS_DICT['FenicsLinearElastic'] = 'pyiron_contrib.continuum.fenics.job.elastic'
 JOB_CLASS_DICT['TrainingContainer'] = 'pyiron_contrib.atomistic.atomistics.job.trainingcontainer'
+JOB_CLASS_DICT['RandomDisMaster'] = 'pyiron_contrib.atomistic.mlip.masters'
+JOB_CLASS_DICT['RandomMDMaster'] = 'pyiron_contrib.atomistic.mlip.masters'
+JOB_CLASS_DICT['MlipSelect'] = 'pyiron_contrib.atomistic.mlip.mlipselect'
+JOB_CLASS_DICT['Mlip'] = 'pyiron_contrib.atomistic.mlip.mlip'
+JOB_CLASS_DICT['LammpsMlip'] = 'pyiron_contrib.atomistic.mlip.lammps'
+JOB_CLASS_DICT['MlipJob'] = 'pyiron_contrib.atomistic.mlip.mlipjob'
 
 
 from ._version import get_versions

pyiron_contrib/atomistic/atomistics/job/trainingcontainer.py

@@ -22,6 +22,7 @@
 >>> container.include_dataset(df)
 
 You can retrieve the full database with :method:`~.TrainingContainer.to_pandas()` like this
+
 >>> container.to_pandas()
 name    atoms   energy  forces  number_of_atoms
 Fe_bcc  ...
@@ -40,6 +41,7 @@ class TrainingContainer(GenericJob):
 
     def __init__(self, project, job_name):
         super().__init__(project=project, job_name=job_name)
+        self.__name__ = "TrainingContainer"
         self._table = pd.DataFrame({
             "name": [],
             "atoms": [],
@@ -85,6 +87,7 @@ def to_pandas(self):
         Export list of structure to pandas table for external fitting codes.
 
         The table contains the following columns:
+            - 'name': human-readable name of the structure
             - 'ase_atoms': the structure as a :class:`.Atoms` object
             - 'energy': the energy of the full structure
             - 'forces': the per atom forces as a :class:`numpy.ndarray`, shape Nx3

pyiron_contrib/atomistic/mlip/cfgs.py

@@ -0,0 +1,148 @@
+# coding: utf-8
+# http://gitlab.skoltech.ru/shapeev/mlip-dev/blob/master/src/external/python/mlippy/cfgs.py
+
+from __future__ import print_function
+import numpy as np
+
+
+class Cfg:
+    pos = None
+    lat = None
+    types = None
+    energy = None
+    forces = None
+    stresses = None
+    desc = None
+    grade = None
+
+
+def readcfg(f):
+    cfg = Cfg()
+    cfg.lat = np.zeros((3, 3))
+    size = -1
+    mode = -1
+    line = f.readline()
+    while line:
+        line = line.upper()
+        line = line.strip()
+        if mode == 0:
+            if line.startswith('SIZE'):
+                line = f.readline()
+                size = int(line.strip())
+                cfg.types = np.zeros(size)
+                cfg.pos = np.zeros((size, 3))
+            elif line.startswith('SUPERCELL'):
+                line = f.readline()
+                vals = line.strip().split()
+                cfg.lat[0, :] = vals[0:3]
+                line = f.readline()
+                vals = line.strip().split()
+                cfg.lat[1, :] = vals[0:3]
+                line = f.readline()
+                vals = line.strip().split()
+                cfg.lat[2, :] = vals[0:3]
+            elif line.startswith('ATOMDATA'):
+                if line.endswith('FZ'):
+                    cfg.forces = np.zeros((size, 3))
+                for i in range(size):
+                    line = f.readline()
+                    vals = line.strip().split()
+                    cfg.types[i] = vals[1]
+                    cfg.pos[i, :] = vals[2:5]
+                    if cfg.forces is not None:
+                        cfg.forces[i, :] = vals[5:8]
+            elif line.startswith('ENERGY'):
+                line = f.readline()
+                cfg.energy = float(line.strip())
+            elif line.startswith('PLUSSTRESS'):
+                line = f.readline()
+                vals = line.strip().split()
+                cfg.stresses = np.zeros(6)
+                cfg.stresses[:] = vals[0:6]
+            elif line.startswith('FEATURE   MV_GRADE'):
+                cfg.grade = float(line.split()[-1])
+            elif line.startswith('FEATURE   PYIRON'):
+                cfg.desc = line.split()[-1]
+        if line.startswith('BEGIN_CFG'):
+            mode = 0
+        elif line.startswith('END_CFG'):
+            break
+        line = f.readline()
+    return cfg
+
+
+def savecfg(f, cfg, desc=None):
+    atstr1 = 'AtomData:  id type       cartes_x      cartes_y      cartes_z           fx          fy          fz'
+    atstr2 = 'AtomData:  id type       cartes_x      cartes_y      cartes_z'
+    size = len(cfg.types)
+    print('BEGIN_CFG', file=f)
+    print('Size', file=f)
+    print('   %-d' % size, file=f)
+    if cfg.lat is not None:
+        print('SuperCell', file=f)
+        for i in range(3):
+            print('         %14f%14f%14f'
+                  % (cfg.lat[i, 0], cfg.lat[i, 1], cfg.lat[i, 2]), file=f)
+    if cfg.forces is not None:
+        print(atstr1, file=f)
+    else:
+        print(atstr2, file=f)
+    for i in range(size):
+        if cfg.forces is not None:
+            print('         %4d %4d %14f%14f%14f %16.8e %16.8e %16.8e' %
+                  (i+1, cfg.types[i], cfg.pos[i, 0], cfg.pos[i, 1], cfg.pos[i, 2],
+                   cfg.forces[i, 0], cfg.forces[i, 1], cfg.forces[i, 2]), file=f)
+        else:
+            print('         %4d %4d %14f%14f%14f' %
+                  (i+1, cfg.types[i], cfg.pos[i, 0], cfg.pos[i, 1], cfg.pos[i, 2]),
+                  file=f)
+    if cfg.energy is not None:
+        print('Energy\t%14f' % cfg.energy, file=f)
+    if cfg.stresses is not None:
+        print('PlusStress:  xx          yy          zz          yz          xz          xy', file=f)
+        print('         %14f%14f%14f%14f%14f%14f' %
+              (cfg.stresses[0], cfg.stresses[1], cfg.stresses[2],
+               cfg.stresses[3], cfg.stresses[4], cfg.stresses[5]), file=f)
+    if desc is not None:
+        print('Feature   from %s' % desc, file=f)
+    if cfg.desc is not None:
+        print('Feature %s' % cfg.desc, file=f)
+    print('END_CFG', file=f)
+
+
+class cfgparser:
+    def __init__(self, file, max_cfgs=None):
+        self.cfgs = []
+        self.file = file
+        self.max_cfgs = max_cfgs
+
+    def __enter__(self):
+        while True:
+            if self.max_cfgs is not None and len(self.cfgs) == self.max_cfgs:
+                break
+            cfg = readcfg(self.file)
+            if cfg.types is not None:
+                self.cfgs.append(cfg)
+            else:
+                break
+        return self.cfgs
+
+    def __exit__(self, *args):
+        self.cfgs = []
+
+
+def printcfg(cfg):
+    savecfg(None, cfg)
+
+
+def loadcfgs(filename, max_cfgs=None):
+    with open(filename, 'r') as file:
+        with cfgparser(file, max_cfgs) as cfgs:
+            return cfgs
+
+
+def savecfgs(filename, cfgs, desc=None):
+    with open(filename, 'w') as file:
+        for cfg in cfgs:
+            savecfg(file, cfg, desc)
+            print("", file=file)

pyiron_contrib/atomistic/mlip/lammps.py

@@ -0,0 +1,126 @@
+# coding: utf-8
+# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+# Distributed under the terms of "New BSD License", see the LICENSE file.
+
+import os
+from pyiron.lammps.base import Input
+from pyiron.lammps.interactive import LammpsInteractive
+from pyiron_contrib.atomistic.mlip.mlip import read_cgfs
+from pyiron_base import GenericParameters
+
+__author__ = "Jan Janssen"
+__copyright__ = "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - " \
+                "Computational Materials Design (CM) Department"
+__version__ = "1.0"
+__maintainer__ = "Jan Janssen"
+__email__ = "janssen@mpie.de"
+__status__ = "development"
+__date__ = "Sep 1, 2018"
+
+
+class LammpsMlip(LammpsInteractive):
+    def __init__(self, project, job_name):
+        super(LammpsMlip, self).__init__(project, job_name)
+        self.input = MlipInput()
+        self.__name__ = "LammpsMlip"
+        self.__version__ = None  # Reset the version number to the executable is set automatically
+        self._executable = None
+        self._executable_activate()
+
+    def set_input_to_read_only(self):
+        """
+        This function enforces read-only mode for the input classes, but it has to be implement in the individual
+        classes.
+        """
+        super(LammpsMlip, self).set_input_to_read_only()
+        self.input.mlip.read_only = True
+
+    def write_input(self):
+        super(LammpsMlip, self).write_input()
+        if self.input.mlip['mlip:load-from'] == 'auto':
+            self.input.mlip['mlip:load-from'] = os.path.basename(self.potential['Filename'][0][0])
+        self.input.mlip.write_file(file_name="mlip.ini", cwd=self.working_directory)
+
+    def enable_active_learning(self):
+        self.input.mlip.load_string("""\
+abinitio void
+mlip mtpr
+mlip:load-from Trained.mtp_
+calculate-efs TRUE
+fit FALSE
+select TRUE
+select:site-en-weight 0.0
+select:energy-weight 1.0
+select:force-weight 0.0
+select:stress-weight 0.0
+select:threshold-init 1e-5
+select:threshold 2.0
+select:threshold-swap 1.000001
+select:threshold-break 5.0
+select:save-selected selected.cfg
+select:save-state selection.mvs
+select:load-state state.mvs
+select:efs-ignored FALSE
+select:log selection.log
+write-cfgs:skip 0
+log lotf.log""")
+
+    def collect_output(self):
+        super(LammpsMlip, self).collect_output()
+        if 'select:save-selected' in self.input.mlip._dataset['Parameter']:
+            file_name = os.path.join(self.working_directory, self.input.mlip['select:save-selected'])
+            if os.path.exists(file_name):
+                cell, positions, forces, stress, energy, indicies, grades, jobids, timesteps = read_cgfs(file_name=file_name)
+                with self.project_hdf5.open("output/mlip") as hdf5_output:
+                    hdf5_output['forces'] = forces
+                    hdf5_output['energy_tot'] = energy
+                    hdf5_output['pressures'] = stress
+                    hdf5_output['cells'] = cell
+                    hdf5_output['positions'] = positions
+                    hdf5_output['indicies'] = indicies
+
+
+class MlipInput(Input):
+    def __init__(self):
+        self.mlip = MlipParameter()
+        super(MlipInput, self).__init__()
+
+    def to_hdf(self, hdf5):
+        """
+        
+        Args:
+            hdf5:
+        Returns:
+        """
+        with hdf5.open("input") as hdf5_input:
+            self.mlip.to_hdf(hdf5_input)
+        super(MlipInput, self).to_hdf(hdf5)
+
+    def from_hdf(self, hdf5):
+        """
+        
+        Args:
+            hdf5:
+        Returns:
+        """
+        with hdf5.open("input") as hdf5_input:
+            self.mlip.from_hdf(hdf5_input)
+        super(MlipInput, self).from_hdf(hdf5)
+
+
+class MlipParameter(GenericParameters):
+    def __init__(self, separator_char=' ', comment_char='#', table_name="mlip_inp"):
+        super(MlipParameter, self).__init__(separator_char=separator_char, comment_char=comment_char, table_name=table_name)
+
+    def load_default(self, file_content=None):
+        if file_content is None:
+            file_content = '''\
+abinitio void
+mlip mtpr
+mlip:load-from auto
+calculate-efs TRUE
+fit FALSE
+select FALSE
+'''
+        self.load_string(file_content)
+