adopting to Python standards
This commit is contained in:
Martin Diehl
parent
20f984fc87
commit
03a81b81e8
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@ -11,195 +11,195 @@ import numpy as np
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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script_name = os.path.splitext(os.path.basename(__file__))[0]
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script_id = ' '.join([script_name,damask.version])
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# Convert .mfd file into a usable format
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# Broken into labeled sections (eg. nodes, links, etc)
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# Each section has a list of labeled elements with formatted numerical data
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def parseMFD(dat):
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formatted = []
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section = 0
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formatted.append({'label': 'header', 'uid': -1, 'els': []})
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# in between =beg= and =end= part of file
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in_block = False
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for line in dat:
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if in_block: # currently in a section
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# lines that start with a space are numerical data
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if line[0] == ' ':
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formatted[section]['els'].append([])
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formatted = []
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section = 0
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formatted.append({'label': 'header', 'uid': -1, 'els': []})
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# in between =beg= and =end= part of file
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in_block = False
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for line in dat:
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if in_block: # currently in a section
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# lines that start with a space are numerical data
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if line[0] == ' ':
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formatted[section]['els'].append([])
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# grab numbers
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nums = re.split(r'\s+', line.strip())
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# grab numbers
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nums = re.split(r'\s+', line.strip())
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for num in nums:
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# floating point has format ' -x.xxxxxxxxxxxxe+yy'
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# scientific notation is used for float
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if (len(num) >= 4) and (num[-4] == 'e'):
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formatted[section]['els'][-1].append(float(num))
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else: # integer
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formatted[section]['els'][-1].append(int(num))
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else: # not numerical data, so it is a label for an element or section end
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if line[0] == '=' and re.search(r'=end=$', line) is not None: # End of section, avoiding regex if possible
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in_block = False
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else:
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formatted[section]['els'].append([])
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formatted[section]['els'][-1] = line
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for num in nums:
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# floating point has format ' -x.xxxxxxxxxxxxe+yy'
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# scientific notation is used for float
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if (len(num) >= 4) and (num[-4] == 'e'):
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formatted[section]['els'][-1].append(float(num))
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else: # integer
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formatted[section]['els'][-1].append(int(num))
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else: # not numerical data, so it is a label for an element or section end
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if line[0] == '=' and re.search(r'=end=$', line) is not None: # End of section, avoiding regex if possible
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in_block = False
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else:
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formatted[section]['els'].append([])
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formatted[section]['els'][-1] = line
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else: # Not in a section, we are looking for a =beg= now
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search = re.search(r'=beg=\s+(\d+)\s\((.*?)\)', line)
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if search is not None: # found start of a new section
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section += 1
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in_block = True
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formatted.append({'label': search.group(2), 'uid': int(search.group(1)), 'els': []})
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else: # No =beg= found, probably in the header
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# Either header or somthing we didn't plan for - just save the line so it isn't lost
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if formatted[section]['uid'] > 0:
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section += 1
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formatted.append({'label': '', 'uid': -2, 'els': []}) # make dummy section to store unrecognized data
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formatted[section]['els'].append(line)
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else: # Not in a section, we are looking for a =beg= now
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search = re.search(r'=beg=\s+(\d+)\s\((.*?)\)', line)
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if search is not None: # found start of a new section
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section += 1
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in_block = True
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formatted.append({'label': search.group(2), 'uid': int(search.group(1)), 'els': []})
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else: # No =beg= found, probably in the header
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# Either header or somthing we didn't plan for - just save the line so it isn't lost
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if formatted[section]['uid'] > 0:
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section += 1
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formatted.append({'label': '', 'uid': -2, 'els': []}) # make dummy section to store unrecognized data
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formatted[section]['els'].append(line)
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return formatted
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return formatted
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def asMFD(mfd_data):
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result = ''
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for section in mfd_data:
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if section['uid'] > 0:
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result += '=beg={0:5d} ({1})\n'.format(section['uid'], section['label'])
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for el in section['els']:
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if type(el) == str:
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result += el
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elif type(el) == list:
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for num in el:
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if type(num) == int:
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result += '{:20d}'.format(num)
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elif type(num) == float:
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result += '{:20.12e}'.format(num)
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else:
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print(f'WARNING: encountered unknown type: {type(el)}')
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result += '\n'
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else:
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print(f'WARNING: encountered unknown type: {type(el)}')
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if section['uid'] > 0:
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result += '=end=\n'
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return result.strip()
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result = ''
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for section in mfd_data:
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if section['uid'] > 0:
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result += '=beg={0:5d} ({1})\n'.format(section['uid'], section['label'])
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for el in section['els']:
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if type(el) == str:
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result += el
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elif type(el) == list:
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for num in el:
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if type(num) == int:
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result += '{:20d}'.format(num)
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elif type(num) == float:
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result += '{:20.12e}'.format(num)
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else:
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print(f'WARNING: encountered unknown type: {type(el)}')
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result += '\n'
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else:
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print(f'WARNING: encountered unknown type: {type(el)}')
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if section['uid'] > 0:
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result += '=end=\n'
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return result.strip()
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def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to add PBC
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base = ['x','y','z']
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box = {'min': np.zeros(3,dtype='d'),
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'max': np.zeros(3,dtype='d'),
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'delta': np.zeros(3,dtype='d'),
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}
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base = ['x','y','z']
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box = {'min': np.zeros(3,dtype='d'),
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'max': np.zeros(3,dtype='d'),
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'delta': np.zeros(3,dtype='d'),
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}
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mfd_dict = {}
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for i in range(len(mfd_data)):
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mfd_dict[mfd_data[i]['label']] = i
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mfd_dict = {}
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for i in range(len(mfd_data)):
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mfd_dict[mfd_data[i]['label']] = i
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NodeCoords = np.array(mfd_data[mfd_dict['nodes']]['els'][1::4])[:,1:4]
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Nnodes = NodeCoords.shape[0]
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NodeCoords = np.array(mfd_data[mfd_dict['nodes']]['els'][1::4])[:,1:4]
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Nnodes = NodeCoords.shape[0]
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box['min'] = NodeCoords.min(axis=0) # find the bounding box
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box['max'] = NodeCoords.max(axis=0)
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box['delta'] = box['max']-box['min']
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for coord in range(3): # calc the dimension of the bounding box
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if box['delta'][coord] != 0.0:
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for extremum in ['min','max']:
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rounded = round(box[extremum][coord]*1e+15/box['delta'][coord]) * \
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1e-15*box['delta'][coord] # rounding to 1e-15 of dimension
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box[extremum][coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros)
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baseNode = {}
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linkNodes = []
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box['min'] = NodeCoords.min(axis=0) # find the bounding box
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box['max'] = NodeCoords.max(axis=0)
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box['delta'] = box['max']-box['min']
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for coord in range(3): # calc the dimension of the bounding box
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if box['delta'][coord] != 0.0:
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for extremum in ['min','max']:
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rounded = round(box[extremum][coord]*1e+15/box['delta'][coord]) * \
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1e-15*box['delta'][coord] # rounding to 1e-15 of dimension
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box[extremum][coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros)
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baseNode = {}
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linkNodes = []
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#-------------------------------------------------------------------------------------------------
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# loop over all nodes
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for node in range(Nnodes):
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key = {}
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maxFlag = [False, False, False]
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Nmax = 0
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Nmin = 0
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for coord in range(3): # for each direction
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if box['delta'][coord] != 0.0:
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rounded = round(NodeCoords[node,coord]*1e+15/box['delta'][coord]) * \
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1e-15*box['delta'][coord] # rounding to 1e-15 of dimension
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NodeCoords[node,coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros)
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key[base[coord]] = "%.8e"%NodeCoords[node,coord] # translate position to string
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if (key[base[coord]] == "%.8e"%box['min'][coord]): # compare to min of bounding box (i.e. is on outer face?)
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Nmin += 1 # count outer (back) face membership
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elif (key[base[coord]] == "%.8e"%box['max'][coord]): # compare to max of bounding box (i.e. is on outer face?)
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Nmax += 1 # count outer (front) face membership
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maxFlag[coord] = True # remember face membership (for linked nodes)
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for node in range(Nnodes):
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key = {}
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maxFlag = [False, False, False]
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Nmax = 0
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Nmin = 0
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for coord in range(3): # for each direction
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if box['delta'][coord] != 0.0:
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rounded = round(NodeCoords[node,coord]*1e+15/box['delta'][coord]) * \
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1e-15*box['delta'][coord] # rounding to 1e-15 of dimension
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NodeCoords[node,coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros)
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key[base[coord]] = "%.8e"%NodeCoords[node,coord] # translate position to string
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if (key[base[coord]] == "%.8e"%box['min'][coord]): # compare to min of bounding box (i.e. is on outer face?)
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Nmin += 1 # count outer (back) face membership
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elif (key[base[coord]] == "%.8e"%box['max'][coord]): # compare to max of bounding box (i.e. is on outer face?)
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Nmax += 1 # count outer (front) face membership
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maxFlag[coord] = True # remember face membership (for linked nodes)
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if Nmin > 0: # node is on a back face
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# prepare for any non-existing entries in the data structure
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if key['x'] not in baseNode.keys():
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baseNode[key['x']] = {}
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if key['y'] not in baseNode[key['x']].keys():
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baseNode[key['x']][key['y']] = {}
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if key['z'] not in baseNode[key['x']][key['y']].keys():
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baseNode[key['x']][key['y']][key['z']] = 0
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if Nmin > 0: # node is on a back face
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# prepare for any non-existing entries in the data structure
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if key['x'] not in baseNode.keys():
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baseNode[key['x']] = {}
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if key['y'] not in baseNode[key['x']].keys():
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baseNode[key['x']][key['y']] = {}
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if key['z'] not in baseNode[key['x']][key['y']].keys():
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baseNode[key['x']][key['y']][key['z']] = 0
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baseNode[key['x']][key['y']][key['z']] = node+1 # remember the base node id
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baseNode[key['x']][key['y']][key['z']] = node+1 # remember the base node id
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if Nmax > 0 and Nmax >= Nmin: # node is on at least as many front than back faces
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if any([maxFlag[i] and active[i] for i in range(3)]):
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linkNodes.append({'id': node+1,'coord': NodeCoords[node], 'faceMember': [maxFlag[i] and active[i] for i in range(3)]})
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if Nmax > 0 and Nmax >= Nmin: # node is on at least as many front than back faces
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if any([maxFlag[i] and active[i] for i in range(3)]):
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linkNodes.append({'id':node+1,'coord':NodeCoords[node],'faceMember':[maxFlag[i] and active[i] for i in range(3)]})
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mfd_data[mfd_dict['entities']]['els'][0][0] += len(linkNodes) * 3
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mfd_data[mfd_dict['entities']]['els'][0][0] += len(linkNodes) * 3
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baseCorner = baseNode["%.8e"%box['min'][0]]["%.8e"%box['min'][1]]["%.8e"%box['min'][2]] # detect ultimate base node
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baseCorner = baseNode["%.8e"%box['min'][0]]["%.8e"%box['min'][1]]["%.8e"%box['min'][2]] # detect ultimate base node
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links = {'uid': 1705, 'label': 'links', 'els': [[7,0],[9,0]]}
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linkID = 0
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for node in linkNodes: # loop over all linked nodes
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linkCoord = [node['coord']] # start list of control node coords with my coords
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for dir in range(3): # check for each direction
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if node['faceMember'][dir]: # me on this front face
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linkCoord[0][dir] = box['min'][dir] # project me onto rear face along dir
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linkCoord.append(np.array(box['min'])) # append base corner
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linkCoord[-1][dir] = box['max'][dir] # stretch it to corresponding control leg of "dir"
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links = {'uid': 1705, 'label': 'links', 'els': [[7,0],[9,0]]}
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linkID = 0
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for node in linkNodes: # loop over all linked nodes
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linkCoord = [node['coord']] # start list of control node coords with my coords
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for dir in range(3): # check for each direction
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if node['faceMember'][dir]: # me on this front face
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linkCoord[0][dir] = box['min'][dir] # project me onto rear face along dir
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linkCoord.append(np.array(box['min'])) # append base corner
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linkCoord[-1][dir] = box['max'][dir] # stretch it to corresponding control leg of "dir"
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nLinks = len(linkCoord)
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for dof in [1,2,3]:
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tied_node = node['id']
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nterms = 1 + nLinks
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nLinks = len(linkCoord)
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for dof in [1,2,3]:
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tied_node = node['id']
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nterms = 1 + nLinks
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linkID += 1
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# Link header
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links['els'].append('link{0}\n'.format(linkID))
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links['els'].append([linkID, 1])
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links['els'].append([0])
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links['els'].append([0])
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links['els'].append([0, 0, 0, tied_node])
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linkID += 1
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# Link header
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links['els'].append('link{0}\n'.format(linkID))
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links['els'].append([linkID, 1])
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links['els'].append([0])
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links['els'].append([0])
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links['els'].append([0, 0, 0, tied_node])
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# these need to be put in groups of four
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link_payload = [dof, 0, nterms]
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# these need to be put in groups of four
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link_payload = [dof, 0, nterms]
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# Individual node contributions (node, dof, coef.)
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for i in range(nterms):
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if i == nLinks:
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link_payload.append(baseCorner)
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else:
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link_payload.append(baseNode["%.8e"%linkCoord[i][0]]["%.8e"%linkCoord[i][1]]["%.8e"%linkCoord[i][2]])
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for i in range(nterms):
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link_payload.append(dof)
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for i in range(nterms):
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if i == nLinks:
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link_payload.append(1.0 - nLinks)
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else:
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link_payload.append(1.0)
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# Individual node contributions (node, dof, coef.)
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for i in range(nterms):
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if i == nLinks:
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link_payload.append(baseCorner)
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else:
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link_payload.append(baseNode["%.8e"%linkCoord[i][0]]["%.8e"%linkCoord[i][1]]["%.8e"%linkCoord[i][2]])
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for i in range(nterms):
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link_payload.append(dof)
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for i in range(nterms):
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if i == nLinks:
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link_payload.append(1.0 - nLinks)
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else:
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link_payload.append(1.0)
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# Needs to be formatted 4 data points per row, character width of 20, so 80 total
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for j in range(0, len(link_payload), 4):
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links['els'].append(link_payload[j:j+4])
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if j+4 < len(link_payload):
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links['els'].append(link_payload[j+4:])
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# Needs to be formatted 4 data points per row, character width of 20, so 80 total
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for j in range(0, len(link_payload), 4):
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links['els'].append(link_payload[j:j+4])
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if j+4 < len(link_payload):
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links['els'].append(link_payload[j+4:])
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i = 0
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while i < len(mfd_data) and mfd_data[i]['uid'] < 1705: i += 1
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i = 0
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while i < len(mfd_data) and mfd_data[i]['uid'] < 1705: i += 1
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if mfd_data[i]['uid'] == 1705: del mfd_data[i]
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mfd_data.insert(i, links)
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if mfd_data[i]['uid'] == 1705: del mfd_data[i]
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mfd_data.insert(i, links)
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#--------------------------------------------------------------------------------------------------
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@ -209,54 +209,54 @@ def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to
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parser = OptionParser(usage='%prog options [file[s]]', description = """
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Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh.
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Use *py_connection to operate on model presently opened in MSC.Mentat.
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""", version = scriptID)
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""", version = script_id)
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parser.add_option('-p', '--port',
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type = int, metavar = 'int', default = None,
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help = 'Mentat connection port')
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type = int, metavar = 'int', default = None,
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help = 'Mentat connection port')
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parser.add_option('-x',
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action = 'store_false', default = True,
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help = 'no PBC along x direction')
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action = 'store_false', default = True,
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help = 'no PBC along x direction')
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parser.add_option('-y',
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action = 'store_false', default = True,
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help = 'no PBC along y direction')
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action = 'store_false', default = True,
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help = 'no PBC along y direction')
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parser.add_option('-z',
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action = 'store_false', default = True,
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help = 'no PBC along z direction')
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action = 'store_false', default = True,
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help = 'no PBC along z direction')
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(options, filenames) = parser.parse_args()
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remote = options.port is not None
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||||
if remote and filenames != []:
|
||||
parser.error('file can not be specified when port is given.')
|
||||
parser.error('file can not be specified when port is given.')
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
if remote:
|
||||
sys.path.append(str(damask.solver.Marc().library_path))
|
||||
import py_mentat
|
||||
sys.path.append(str(damask.solver.Marc().library_path))
|
||||
import py_mentat
|
||||
|
||||
print(scriptName+': waiting to connect...')
|
||||
filenames = [os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()) + '.mfd')]
|
||||
try:
|
||||
py_mentat.py_connect('',options.port)
|
||||
py_mentat.py_send('*set_save_formatted on')
|
||||
py_mentat.py_send('*save_as_model "{}" yes'.format(filenames[0]))
|
||||
py_mentat.py_get_int("nnodes()")
|
||||
except py_mentat.InputError as err:
|
||||
print(f'{err}. Try Tools/Python/"Run as Separate Process" & "Initiate".')
|
||||
sys.exit(-1)
|
||||
print( 'connected...')
|
||||
print(script_name+': waiting to connect...')
|
||||
filenames = [os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()) + '.mfd')]
|
||||
try:
|
||||
py_mentat.py_connect('',options.port)
|
||||
py_mentat.py_send('*set_save_formatted on')
|
||||
py_mentat.py_send('*save_as_model "{}" yes'.format(filenames[0]))
|
||||
py_mentat.py_get_int("nnodes()")
|
||||
except py_mentat.InputError as err:
|
||||
print(f'{err}. Try Tools/Python/"Run as Separate Process" & "Initiate".')
|
||||
sys.exit(-1)
|
||||
print( 'connected...')
|
||||
|
||||
for name in filenames:
|
||||
while remote and not os.path.exists(name): time.sleep(0.5)
|
||||
with open( name,'r') if name is not None else sys.stdin as fileIn:
|
||||
print(scriptName+': '+name)
|
||||
mfd = parseMFD(fileIn)
|
||||
while remote and not os.path.exists(name): time.sleep(0.5)
|
||||
with open( name,'r') if name is not None else sys.stdin as file_in:
|
||||
print(script_name+': '+name)
|
||||
mfd = parseMFD(file_in)
|
||||
|
||||
add_servoLinks(mfd,[options.x,options.y,options.z])
|
||||
with open( name,'w') if name is not None else sys.stdout as fileOut:
|
||||
fileOut.write(asMFD(mfd))
|
||||
add_servoLinks(mfd,[options.x,options.y,options.z])
|
||||
with open( name,'w') if name is not None else sys.stdout as file_out:
|
||||
file_out.write(asMFD(mfd))
|
||||
|
||||
if remote:
|
||||
py_mentat.py_send('*open_model "{}"'.format(filenames[0]))
|
||||
py_mentat.py_send('*open_model "{}"'.format(filenames[0]))
|
||||
|
|
|
|||
|
|
@ -7,8 +7,8 @@ from optparse import OptionParser
|
|||
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
script_name = os.path.splitext(os.path.basename(__file__))[0]
|
||||
script_id = ' '.join([script_name,damask.version])
|
||||
|
||||
#-------------------------------------------------------------------------------------------------
|
||||
def outMentat(cmd,locals):
|
||||
|
|
@ -45,7 +45,7 @@ def output(cmds,locals,dest):
|
|||
#-------------------------------------------------------------------------------------------------
|
||||
def init():
|
||||
return [
|
||||
"|"+' '.join([scriptID] + sys.argv[1:]),
|
||||
"|"+' '.join([script_id] + sys.argv[1:]),
|
||||
"*draw_manual", # prevent redrawing in Mentat, should be much faster
|
||||
"*new_model yes",
|
||||
"*reset",
|
||||
|
|
@ -170,7 +170,7 @@ def initial_conditions(material):
|
|||
parser = OptionParser(usage='%prog options [file[s]]', description = """
|
||||
Generate MSC.Marc FE hexahedral mesh from geom file.
|
||||
|
||||
""", version = scriptID)
|
||||
""", version = script_id)
|
||||
|
||||
parser.add_option('-p', '--port',
|
||||
dest = 'port',
|
||||
|
|
@ -194,7 +194,7 @@ if options.port is not None:
|
|||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
print(scriptName+': '+name)
|
||||
print(script_name+': '+name)
|
||||
|
||||
geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
material = geom.material.flatten(order='F')
|
||||
|
|
@ -211,11 +211,11 @@ for name in filenames:
|
|||
'*draw_automatic',
|
||||
]
|
||||
|
||||
outputLocals = {}
|
||||
output_locals = {}
|
||||
if options.port:
|
||||
py_mentat.py_connect('',options.port)
|
||||
output(cmds,outputLocals,'Mentat')
|
||||
output(cmds,output_locals,'Mentat')
|
||||
py_mentat.py_disconnect()
|
||||
else:
|
||||
with sys.stdout if name is None else open(os.path.splitext(name)[0]+'.proc','w') as f:
|
||||
output(cmds,outputLocals,f)
|
||||
output(cmds,output_locals,f)
|
||||
|
|
|
|||
Loading…
Reference in New Issue