diff --git a/parser/parser-lib-atoms/libAtomsParser.py b/parser/parser-lib-atoms/libAtomsParser.py
index f813e01f4fdb7f025736cf854f3bbc599fec2f6b..f94c19effd970ffd60c36869112c0c355c9d0ace 100644
--- a/parser/parser-lib-atoms/libAtomsParser.py
+++ b/parser/parser-lib-atoms/libAtomsParser.py
@@ -67,7 +67,7 @@ def parse(output_file_name):
base_dir = os.path.dirname(os.path.abspath(output_file_name))
terminal_gap = LibAtomsGapParser(osio)
- terminal_gap.ParseOutput(output_file_name)
+ terminal_gap.ParseOutput(output_file_name, base_dir)
terminal_trj = terminal_gap.trj
@@ -81,6 +81,68 @@ def parse(output_file_name):
push(jbe, gap, 'program_name')
push(jbe, gap, 'program_version', key2='GAP_params.svn_version')
+ # SYSTEM DESCRIPTION
+ refs_system_description = []
+ all_frames = trj.frames # <- Initial config + trajectory
+ for frame in all_frames:
+ with open_section(jbe, 'section_system') as gid:
+ refs_system_description.append(gid)
+ # Configuration core
+ atom_labels = np.array(frame.ase_config.get_chemical_symbols())
+ push_array_values(jbe, atom_labels, 'atom_labels')
+ push_array_values(jbe, frame.ase_config.get_positions(), 'atom_positions')
+ # CAREFUL, OBSERVE CELL CONVENTION: 1st index -> x,y,z, 2nd index -> a,b,c
+ # Hence use transpose here:
+ push_array_values(jbe, frame.ase_config.get_cell().T, 'simulation_cell')
+ push_array_values(jbe, frame.ase_config.get_pbc(), 'configuration_periodic_dimensions')
+ if frame.ase_config.has('velocities'):
+ push_array_values(jbe, frame.ase_config.get_velocities(), 'atom_velocities')
+ if frame.ase_config.has('forces'):
+ # TODO Wouldn't it be nicer if forces were added here?
+ pass
+ pass
+
+ # SINGLE CONFIGURATIONS
+ refs_single_configuration = []
+ i_frame = -1
+ for frame in all_frames:
+ i_frame += 1
+ with open_section(jbe, 'section_single_configuration_calculation') as gid:
+ refs_single_configuration.append(gid)
+ # Reference system description section
+ ref_system = refs_system_description[i_frame]
+ push_value(jbe, ref_system, 'single_configuration_calculation_to_system_ref')
+ # Energy
+ if frame.has_energy:
+ push_value(jbe, frame.energy, 'energy_total') # TODO Check units
+ # Virial
+ if frame.has_virial:
+ push_array_values(jbe, frame.virial, 'x_lib_atoms_virial_tensor')
+ # Forces
+ if frame.ase_config.has('forces'):
+ push_array_values(jbe, frame.ase_config.get_forces(), 'atom_forces')
+ # Type label
+ if frame.has_config_type:
+ push_value(jbe, frame.config_type, 'x_lib_atoms_config_type')
+ pass
+
+ # GAP DESCRIPTION
+ if gap.has_gap_data:
+ with open_section(jbe, 'x_lib_atoms_section_gap') as gap_gid:
+ push_array_values(jbe, np.array(refs_single_configuration), 'x_lib_atoms_training_config_refs')
+ push_value(jbe, gap['GAP_params.label'].As(), 'x_lib_atoms_GAP_params_label')
+ push_value(jbe, gap['GAP_params.svn_version'].As(), 'x_lib_atoms_GAP_params_svn_version')
+ push_value(jbe, gap['GAP_data.do_core'].As(), 'x_lib_atoms_GAP_data_do_core')
+ push_value(jbe, gap['GAP_data.e0'].As(float), 'x_lib_atoms_GAP_data_e0')
+ push_value(jbe, gap['command_line.command_line'].As(), 'x_lib_atoms_command_line_command_line')
+ push_value(jbe, gap['gpSparse.n_coordinate'].As(int), 'x_lib_atoms_gpSparse_n_coordinate')
+ types = [int, int, int, str, float, float, float, str, str, float, str, int, int ]
+ keys = ['n_sparseX', 'dimensions', 'n_permutations', 'sparsified', 'signal_variance', 'signal_mean', 'covariance_type', 'label', 'sparseX_filename', 'theta', 'descriptor', 'perm.permutation', 'perm.i']
+ for i,key in enumerate(keys):
+ push_value(jbe, gap['gpCoordinates.%s' % key].As(types[i]), 'x_lib_atoms_gpCoordinates_%s' % key.replace('.', '_'))
+ for key in ['alpha', 'sparseX']:
+ push_array_values(jbe, gap['gpCoordinates.%s' % key].As(), 'x_lib_atoms_gpCoordinates_%s' % key.replace('.', '_'))
+
jbe.finishedParsingSession("ParseSuccess", None)
return
diff --git a/parser/parser-lib-atoms/libLibAtomsParser.py b/parser/parser-lib-atoms/libLibAtomsParser.py
index f11e3ada53a330df947e4442df28db6ae12495de..577ec45464f4297a4b6cd0d402ff4ef48d863e31 100644
--- a/parser/parser-lib-atoms/libLibAtomsParser.py
+++ b/parser/parser-lib-atoms/libLibAtomsParser.py
@@ -176,8 +176,9 @@ class LibAtomsGapParser(LibAtomsParser):
super(LibAtomsGapParser, self).__init__(log)
self.logtag = 'gap-xml'
self.trj = None
+ self.has_gap_data = False
return
- def ParseOutput(self, output_file):
+ def ParseOutput(self, output_file, base_dir=''):
self.Set('program_name', 'libAtoms')
dom = xml.dom.minidom.parse(output_file)
root = XmlGetUnique(dom, 'GAP_params')
@@ -210,6 +211,7 @@ class LibAtomsGapParser(LibAtomsParser):
# 'GAP_params/gpSparse'
key = 'gpSparse'
if key in child_nodes:
+ self.has_gap_data = True
node = child_nodes[key][0]
atts = XmlGetAttributes(node)
keys = ['n_coordinate']
@@ -249,6 +251,7 @@ class LibAtomsGapParser(LibAtomsParser):
n_sparseX = self['gpCoordinates.n_sparseX'].As(int)
n_dim = self['gpCoordinates.dimensions'].As(int)
sparseX_filename = self['gpCoordinates.sparseX_filename'].As(str)
+ sparseX_filename = os.path.join(base_dir, sparseX_filename)
# Read alpha coefficients
nodes = gp_coord_child_nodes[key]
alpha_cutoff = np.zeros((n_sparseX, 2), dtype='float64')
@@ -315,8 +318,31 @@ class LibAtomsFrame(LibAtomsParser):
def __init__(self, log=None):
super(LibAtomsFrame, self).__init__(log)
self.ase_config = None
+ self.has_energy = False
+ self.energy = None
+ self.has_virial = False
+ self.virial = None
+ self.has_config_type = False
+ self.config_type = None
def LoadAseConfig(self, ase_config):
- self.ase_atoms = ase_config
+ self.ase_config = ase_config
+ key = 'energy'
+ if key in self.ase_config.info:
+ has_energy = True
+ self.energy = self.ase_config.info[key]
+ key = 'config_type'
+ if key in self.ase_config.info:
+ self.has_config_type = True
+ self.config_type = self.ase_config.info[key]
+ key = 'virial'
+ if key in self.ase_config.info:
+ self.has_virial = True
+ self.virial = np.array(self.ase_config.info[key])
+
+
+
+
+
return
# ===================