Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
This commit is contained in:
Franz Roters
commit
dd34f28cdb
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@ -1,67 +1,103 @@
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#!/usr/bin/env python2.7
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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# -*- coding: UTF-8 no BOM -*-
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import sys,os
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from __future__ import print_function
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import sys,os,re,time,tempfile
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import numpy as np
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import numpy as np
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from optparse import OptionParser
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import argparse
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import damask
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import damask
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sys.path.append(damask.solver.Marc().libraryPath())
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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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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scriptID = ' '.join([scriptName,damask.version])
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sys.path.append(damask.solver.Marc().libraryPath())
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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(fname):
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formatted = []
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with open(fname,'r') as dat:
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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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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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return formatted
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active=[True,True,True] # directions on which to add PBC
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def asMFD(mfd_data):
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def outMentat(cmd,locals):
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result = ''
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if cmd[0:3] == '(!)':
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for section in mfd_data:
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exec(cmd[3:])
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if section['uid'] > 0:
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elif cmd[0:3] == '(?)':
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result += '=beg={0:5d} ({1})\n'.format(section['uid'], section['label'])
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cmd = eval(cmd[3:])
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for el in section['els']:
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py_mentat.py_send(cmd)
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if type(el) == str:
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else:
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result += el
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py_mentat.py_send(cmd)
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elif type(el) == list:
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return
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for num in el:
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if type(num) == int:
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#-------------------------------------------------------------------------------------------------
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result += '{:20d}'.format(num)
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def outFile(cmd,locals,dest):
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elif type(num) == float:
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if cmd[0:3] == '(!)':
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result += '{:20.12e}'.format(num)
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exec(cmd[3:])
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else:
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elif cmd[0:3] == '(?)':
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damask.util.croak('WARNING: encountered unknown type: ' + str(type(el)))
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cmd = eval(cmd[3:])
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result += '\n'
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dest.write(cmd+'\n')
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else:
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dest.write(cmd+'\n')
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return
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#-------------------------------------------------------------------------------------------------
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def output(cmds,locals,dest):
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for cmd in cmds:
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if isinstance(cmd,list):
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output(cmd,locals,dest)
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else:
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if dest == 'Mentat':
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outMentat(str(cmd),locals)
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else:
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else:
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outFile(str(cmd),locals,dest)
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damask.util.croak('WARNING: encountered unknown type: ' + str(type(el)))
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return
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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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def servoLink():
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cmds = []
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base = ['x','y','z']
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base = ['x','y','z']
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box = {'min': np.zeros(3,dtype='d'),
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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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'max': np.zeros(3,dtype='d'),
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'delta': np.zeros(3,dtype='d'),
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'delta': np.zeros(3,dtype='d'),
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}
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}
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Nnodes = py_mentat.py_get_int("nnodes()")
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NodeCoords = np.zeros((Nnodes,3),dtype='d')
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mfd_dict = {}
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for node in range(Nnodes):
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for i in range(len(mfd_data)):
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NodeCoords[node,0] = py_mentat.py_get_float("node_x(%i)"%(node+1))
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mfd_dict[mfd_data[i]['label']] = i
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NodeCoords[node,1] = py_mentat.py_get_float("node_y(%i)"%(node+1))
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NodeCoords[node,2] = py_mentat.py_get_float("node_z(%i)"%(node+1))
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NodeCoords = np.array(mfd_data[mfd_dict['nodes']]['els'][0::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['min'] = NodeCoords.min(axis=0) # find the bounding box
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box['max'] = NodeCoords.max(axis=0)
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box['max'] = NodeCoords.max(axis=0)
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box['delta'] = box['max']-box['min']
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box['delta'] = box['max']-box['min']
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@ -108,9 +144,12 @@ def servoLink():
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if any([maxFlag[i] and active[i] for i in range(3)]):
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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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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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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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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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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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for dir in range(3): # check for each direction
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@ -121,77 +160,100 @@ def servoLink():
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nLinks = len(linkCoord)
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nLinks = len(linkCoord)
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for dof in [1,2,3]:
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for dof in [1,2,3]:
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cmds.append([
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tied_node = node['id']
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"*new_link *link_class servo",
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nterms = 1 + nLinks
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"*link_class servo *tied_node %i"%node['id'],
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"*link_class servo *tied_dof %i"%dof,
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linkID += 1
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"*servo_nterms %i"%(1+nLinks),
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# Link header
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])
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links['els'].append('link{0}\n'.format(linkID))
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for i in range(nLinks):
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links['els'].append([linkID, 1])
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cmds.append([
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links['els'].append([0])
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"*link_class servo *servo_ret_node %i %i"\
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links['els'].append([0])
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%(i+1,baseNode["%.8e"%linkCoord[i][0]]["%.8e"%linkCoord[i][1]]["%.8e"%linkCoord[i][2]]),
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links['els'].append([0, 0, 0, tied_node])
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"*link_class servo *servo_ret_dof %i %i"%(i+1,dof),
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"*link_class servo *servo_ret_coef %i 1"%(i+1),
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# these need to be put in groups of four
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])
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link_payload = [dof, 0, nterms]
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cmds.append([
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"*link_class servo *servo_ret_node %i %i"%(1+nLinks,baseCorner),
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# Individual node contributions (node, dof, coef.)
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"*link_class servo *servo_ret_dof %i %i"%(1+nLinks,dof),
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for i in range(nterms):
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"*link_class servo *servo_ret_coef %i -%i"%(1+nLinks,nLinks-1),
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if i == nLinks:
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])
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link_payload.append(baseCorner)
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return cmds
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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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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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#--------------------------------------------------------------------------------------------------
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#--------------------------------------------------------------------------------------------------
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# MAIN
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# MAIN
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#--------------------------------------------------------------------------------------------------
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage = '%prog [options]', description = """
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parser = argparse.ArgumentParser(description = """
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Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh presently opened in MSC.Mentat
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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 = scriptID)
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parser.add_option("-p", "--port", type="int", dest="port", metavar='int',
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parser.add_argument('-p', '--port',
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help="Mentat connection port [%default]")
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type = int, metavar = 'int', default = None,
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parser.add_option("-v", "--verbose", action="store_true", dest="verbose",
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help = 'Mentat connection port')
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help="write Mentat command stream also to stdout [%default]")
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parser.add_argument('-x',
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parser.set_defaults(port = 40007,
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action = 'store_false',
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verbose = False)
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help = 'no PBC along x direction')
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parser.add_argument('-y',
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action = 'store_false',
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help = 'no PBC along y direction')
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parser.add_argument('-z',
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action = 'store_false',
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help = 'no PBC along z direction')
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parser.add_argument('file', nargs='*',
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help = 'Mentat formatted data (.mfd) file[s] to add periodic boundary conditions to')
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(options, args) = parser.parse_args()
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args = parser.parse_args()
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try:
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remote = args.port is not None
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import py_mentat
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except:
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damask.util.croak('error: no valid Mentat release found')
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sys.exit(-1)
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outputLocals = {}
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if remote:
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try: import py_mentat
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except:
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damask.util.croak('no valid Mentat release found.')
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sys.exit(-1)
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damask.util.report(scriptName,'waiting to connect...')
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damask.util.report(scriptName, 'waiting to connect...')
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args.file = [os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()) + '.mfd')]
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try:
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py_mentat.py_connect('',args.port)
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py_mentat.py_send('*set_save_formatted on')
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py_mentat.py_send('*save_as_model "{}" yes'.format(args.file[0]))
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py_mentat.py_get_int("nnodes()") # hopefully blocks until file is written
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except:
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damask.util.croak('failed. try setting Tools/Python/"Run as Separate Process" & "Initiate".')
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sys.exit()
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damask.util.croak( 'connected...')
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try:
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for mfdfile in args.file:
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py_mentat.py_connect('',options.port)
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while remote and not os.path.exists(mfdfile): time.sleep(0.5) # wait for Mentat to write MFD file
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# prevent redrawing in Mentat, should be much faster.
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damask.util.report(scriptName, mfdfile)
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# Since py_connect has no return value, try this to determine if failed or not
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mfd = parseMFD(mfdfile)
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output(['*draw_manual'],outputLocals,'Mentat')
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add_servoLinks(mfd,[args.x,args.y,args.z])
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except:
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with open(mfdfile, 'w') as file:
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damask.util.croak('Could not connect. Set Tools/Python/"Run as Separate Process" & "Initiate"...')
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file.write(asMFD(mfd))
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sys.exit()
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damask.util.croak('connected...')
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if remote:
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try: py_mentat.py_send('*open_model "{}"'.format(args.file[0]))
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output(['*remove_all_servos',
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except: damask.util.croak('lost connection on sending open command for "{}".'.format(args.file[0]))
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'*sweep_all',
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'*renumber_nodes',
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'*set_links off',
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],outputLocals,'Mentat') # script depends on consecutive numbering of nodes
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cmds = servoLink()
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output(cmds,outputLocals,'Mentat')
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output(['*draw_automatic',
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],outputLocals,'Mentat') # script depends on consecutive numbering of nodes
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py_mentat.py_disconnect()
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if options.verbose:
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output(cmds,outputLocals,sys.stdout)
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