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Dynearthsol.py
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Dynearthsol.py
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#!/usr/bin/env python
from __future__ import print_function, unicode_literals
import sys
import numpy as np
# 2D or 3D data?
ndims = 2
class Dynearthsol:
'''Read output file of 2D/3D DynEarthSol'''
def __init__(self, modelname):
self.suffix = 'save'
self.modelname = modelname
self.read_info()
self.read_header(self.frames[0])
return
def read_info(self):
tmp = np.fromfile(self.modelname + '.info', dtype=float, sep=' ')
tmp.shape = (-1, 8)
self.frames = list(tmp[:,0].astype(int))
self.steps = list(tmp[:,1].astype(int))
self.time = list(tmp[:,2].astype(float))
self.nnode_list = tmp[:,5].astype(int)
self.nelem_list = tmp[:,6].astype(int)
return
def get_fn(self, frame):
return '{0}.{1}.{2:0=6}'.format(self.modelname, self.suffix, frame)
def read_header(self, frame):
self._header_frame = frame
headerlen = 4096
fname = self.get_fn(frame)
with open(fname, 'rb') as f:
header = f.read(headerlen).splitlines()
#print(header)
# parsing 1st line
first = header[0].split(b' ')
if (first[0] != b'#' or
first[1] != b'DynEarthSol' or
first[2].split(b'=')[0] != b'ndims' or
first[3].split(b'=')[0] != b'revision'):
print('Error:', fname, 'is not a valid DynEarthSol output file!')
sys.exit(1)
self.ndims = int(first[2].split(b'=')[1])
self.revision = int(first[3].split(b'=')[1])
if self.ndims == 2:
self.nstr = 3
self.component_names = ('XX', 'ZZ', 'XZ')
else:
self.nstr = 6
self.component_names = ('XX', 'YY', 'ZZ', 'XY', 'XZ', 'YZ')
# parsing other lines
self.field_pos = {}
for line in header[1:]:
# test for null in python3 bytes and python2 str
if line[0] in (0, '\x00'): break # end of record
name, pos = line.split(b'\t')
self.field_pos[name.decode('ascii')] = int(pos)
#print(self.field_pos)
return
def _get_dtype_count_shape(self, frame, name):
i = self.frames.index(frame)
nnode = self.nnode_list[i]
nelem = self.nelem_list[i]
dtype = np.float64 if name not in ('connectivity', 'bcflag') else np.int32
if name in set(['strain', 'strain-rate', 'stress', 'stress averaged']):
count = self.nstr * nelem
shape = (nelem, self.nstr)
elif name in set(['density', 'material', 'mesh quality',
'plastic strain', 'plastic strain-rate',
'viscosity', 'edvoldt', 'volume']):
count = nelem
shape = (nelem, )
elif name in set(['connectivity']):
count = (self.ndims + 1) * nelem
shape = (nelem, self.ndims+1)
elif name in set(['coordinate', 'velocity', 'velocity averaged', 'force', 'coord0']):
count = self.ndims * nnode
shape = (nnode, self.ndims)
elif name in set(['bcflag', 'temperature', 'mass', 'tmass', 'volume_n']):
count = nnode
shape = (nnode, )
else:
raise NameError('uknown field name: ' + name)
return dtype, count, shape
def read_field(self, frame, name):
if frame != self._header_frame: self.read_header(frame)
dtype, count, shape = self._get_dtype_count_shape(frame, name)
pos = self.field_pos[name]
fname = self.get_fn(frame)
with open(fname,'r') as f:
f.seek(pos)
field = np.fromfile(f, dtype=dtype, count=count).reshape(shape)
return field
def overwrite_field(self, frame, name, data):
if frame != self._header_frame: self.read_header(frame)
if frame != self._header_frame: read_header(frame)
if name.startswith(('markerset.', 'hydrous-markerset.')):
dtype = data.dtype
count = len(data)
shape = (count,)
else:
dtype, count, shape = self._get_dtype_count_shape(frame, name)
if data.shape != shape:
raise Error('Shape of {0} field is changed! Expecting {1}, got {2}.'.format(name, shape, data.shape))
pos = self.field_pos[name]
fname = self.get_fn(frame)
with open(fname, 'r+') as f:
f.seek(pos)
f.write(data.tostring())
return
def read_markers(self, frame, markername):
'Read and return marker data'
if frame != self._header_frame: self.read_header(frame)
fname = self.get_fn(frame)
with open(fname) as f:
pos = self.field_pos[markername+' size']
f.seek(pos)
nmarkers = np.fromfile(f, dtype=np.int32, count=1)[0]
marker_data = {'size': nmarkers}
# floating point
for name in (markername+'.coord',):
pos = self.field_pos[name]
f.seek(pos)
tmp = np.fromfile(f, dtype=np.float64, count=nmarkers*self.ndims)
marker_data[name] = tmp.reshape(-1, self.ndims)
#print(marker_data[name].shape, marker_data[name])
# int
for name in (markername+'.elem', markername+'.mattype', markername+'.id'):
pos = self.field_pos[name]
f.seek(pos)
marker_data[name] = np.fromfile(f, dtype=np.int32, count=nmarkers)
#print(marker_data[name].shape, marker_data[name])
return marker_data
class DynearthsolCheckpoint(Dynearthsol):
'''Read chkpt file of 2D/3D DynEarthSol'''
def __init__(self, modelname, frame):
self.suffix = 'chkpt'
self.modelname = modelname
self.read_info()
self.read_header(frame)
return
def _get_dtype_count_shape(self, frame, name):
i = self.frames.index(frame)
nnode = self.nnode_list[i]
nelem = self.nelem_list[i]
dtype = np.float64 if name != 'connectivity' else np.int32
if name in set(['volume_old']):
count = nelem
shape = (nelem, )
else:
raise NameError('uknown field name: ' + name)
return dtype, count, shape
def read_markers(self, frame, markername):
'Read and return marker data'
if frame != self._header_frame: read_header(frame)
fname = self.get_fn(frame)
with open(fname) as f:
pos = self.field_pos[markername+' size']
f.seek(pos)
nmarkers = np.fromfile(f, dtype=np.int32, count=1)[0]
marker_data = {'size': nmarkers}
# floating point
for name in (markername+'.eta',):
pos = self.field_pos[name]
f.seek(pos)
tmp = np.fromfile(f, dtype=np.float64, count=nmarkers*(self.ndims+1))
marker_data[name] = tmp.reshape(-1, self.ndims+1)
#print(marker_data[name].shape, marker_data[name])
# int
for name in (markername+'.elem', markername+'.mattype', markername+'.id'):
pos = self.field_pos[name]
f.seek(pos)
marker_data[name] = np.fromfile(f, dtype=np.int32, count=nmarkers)
#print(marker_data[name].shape, marker_data[name])
return marker_data