From 03a81b81e86d9212fdd4871b78ab661442a8fcc5 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 28 Nov 2022 09:21:47 +0100 Subject: [PATCH] adopting to Python standards --- processing/mentat_pbcOnBoxMesh.py | 374 +++++++++++++++--------------- processing/mentat_spectralBox.py | 16 +- 2 files changed, 195 insertions(+), 195 deletions(-) diff --git a/processing/mentat_pbcOnBoxMesh.py b/processing/mentat_pbcOnBoxMesh.py index 1cf18eeda..3eedacb7d 100755 --- a/processing/mentat_pbcOnBoxMesh.py +++ b/processing/mentat_pbcOnBoxMesh.py @@ -11,195 +11,195 @@ import numpy as np 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]) # Convert .mfd file into a usable format # Broken into labeled sections (eg. nodes, links, etc) # Each section has a list of labeled elements with formatted numerical data def parseMFD(dat): - formatted = [] - section = 0 - formatted.append({'label': 'header', 'uid': -1, 'els': []}) - # in between =beg= and =end= part of file - in_block = False - for line in dat: - if in_block: # currently in a section - # lines that start with a space are numerical data - if line[0] == ' ': - formatted[section]['els'].append([]) + formatted = [] + section = 0 + formatted.append({'label': 'header', 'uid': -1, 'els': []}) + # in between =beg= and =end= part of file + in_block = False + for line in dat: + if in_block: # currently in a section + # lines that start with a space are numerical data + if line[0] == ' ': + formatted[section]['els'].append([]) - # grab numbers - nums = re.split(r'\s+', line.strip()) + # grab numbers + nums = re.split(r'\s+', line.strip()) - for num in nums: - # floating point has format ' -x.xxxxxxxxxxxxe+yy' - # scientific notation is used for float - if (len(num) >= 4) and (num[-4] == 'e'): - formatted[section]['els'][-1].append(float(num)) - else: # integer - formatted[section]['els'][-1].append(int(num)) - else: # not numerical data, so it is a label for an element or section end - if line[0] == '=' and re.search(r'=end=$', line) is not None: # End of section, avoiding regex if possible - in_block = False - else: - formatted[section]['els'].append([]) - formatted[section]['els'][-1] = line + for num in nums: + # floating point has format ' -x.xxxxxxxxxxxxe+yy' + # scientific notation is used for float + if (len(num) >= 4) and (num[-4] == 'e'): + formatted[section]['els'][-1].append(float(num)) + else: # integer + formatted[section]['els'][-1].append(int(num)) + else: # not numerical data, so it is a label for an element or section end + if line[0] == '=' and re.search(r'=end=$', line) is not None: # End of section, avoiding regex if possible + in_block = False + else: + formatted[section]['els'].append([]) + formatted[section]['els'][-1] = line - else: # Not in a section, we are looking for a =beg= now - search = re.search(r'=beg=\s+(\d+)\s\((.*?)\)', line) - if search is not None: # found start of a new section - section += 1 - in_block = True - formatted.append({'label': search.group(2), 'uid': int(search.group(1)), 'els': []}) - else: # No =beg= found, probably in the header - # Either header or somthing we didn't plan for - just save the line so it isn't lost - if formatted[section]['uid'] > 0: - section += 1 - formatted.append({'label': '', 'uid': -2, 'els': []}) # make dummy section to store unrecognized data - formatted[section]['els'].append(line) + else: # Not in a section, we are looking for a =beg= now + search = re.search(r'=beg=\s+(\d+)\s\((.*?)\)', line) + if search is not None: # found start of a new section + section += 1 + in_block = True + formatted.append({'label': search.group(2), 'uid': int(search.group(1)), 'els': []}) + else: # No =beg= found, probably in the header + # Either header or somthing we didn't plan for - just save the line so it isn't lost + if formatted[section]['uid'] > 0: + section += 1 + formatted.append({'label': '', 'uid': -2, 'els': []}) # make dummy section to store unrecognized data + formatted[section]['els'].append(line) - return formatted + return formatted def asMFD(mfd_data): - result = '' - for section in mfd_data: - if section['uid'] > 0: - result += '=beg={0:5d} ({1})\n'.format(section['uid'], section['label']) - for el in section['els']: - if type(el) == str: - result += el - elif type(el) == list: - for num in el: - if type(num) == int: - result += '{:20d}'.format(num) - elif type(num) == float: - result += '{:20.12e}'.format(num) - else: - print(f'WARNING: encountered unknown type: {type(el)}') - result += '\n' - else: - print(f'WARNING: encountered unknown type: {type(el)}') - if section['uid'] > 0: - result += '=end=\n' - return result.strip() + result = '' + for section in mfd_data: + if section['uid'] > 0: + result += '=beg={0:5d} ({1})\n'.format(section['uid'], section['label']) + for el in section['els']: + if type(el) == str: + result += el + elif type(el) == list: + for num in el: + if type(num) == int: + result += '{:20d}'.format(num) + elif type(num) == float: + result += '{:20.12e}'.format(num) + else: + print(f'WARNING: encountered unknown type: {type(el)}') + result += '\n' + else: + print(f'WARNING: encountered unknown type: {type(el)}') + if section['uid'] > 0: + result += '=end=\n' + return result.strip() def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to add PBC - base = ['x','y','z'] - box = {'min': np.zeros(3,dtype='d'), - 'max': np.zeros(3,dtype='d'), - 'delta': np.zeros(3,dtype='d'), - } + base = ['x','y','z'] + box = {'min': np.zeros(3,dtype='d'), + 'max': np.zeros(3,dtype='d'), + 'delta': np.zeros(3,dtype='d'), + } - mfd_dict = {} - for i in range(len(mfd_data)): - mfd_dict[mfd_data[i]['label']] = i + mfd_dict = {} + for i in range(len(mfd_data)): + mfd_dict[mfd_data[i]['label']] = i - NodeCoords = np.array(mfd_data[mfd_dict['nodes']]['els'][1::4])[:,1:4] - Nnodes = NodeCoords.shape[0] + NodeCoords = np.array(mfd_data[mfd_dict['nodes']]['els'][1::4])[:,1:4] + Nnodes = NodeCoords.shape[0] - box['min'] = NodeCoords.min(axis=0) # find the bounding box - box['max'] = NodeCoords.max(axis=0) - box['delta'] = box['max']-box['min'] - for coord in range(3): # calc the dimension of the bounding box - if box['delta'][coord] != 0.0: - for extremum in ['min','max']: - rounded = round(box[extremum][coord]*1e+15/box['delta'][coord]) * \ - 1e-15*box['delta'][coord] # rounding to 1e-15 of dimension - box[extremum][coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros) - baseNode = {} - linkNodes = [] + box['min'] = NodeCoords.min(axis=0) # find the bounding box + box['max'] = NodeCoords.max(axis=0) + box['delta'] = box['max']-box['min'] + for coord in range(3): # calc the dimension of the bounding box + if box['delta'][coord] != 0.0: + for extremum in ['min','max']: + rounded = round(box[extremum][coord]*1e+15/box['delta'][coord]) * \ + 1e-15*box['delta'][coord] # rounding to 1e-15 of dimension + box[extremum][coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros) + baseNode = {} + linkNodes = [] #------------------------------------------------------------------------------------------------- # loop over all nodes - for node in range(Nnodes): - key = {} - maxFlag = [False, False, False] - Nmax = 0 - Nmin = 0 - for coord in range(3): # for each direction - if box['delta'][coord] != 0.0: - rounded = round(NodeCoords[node,coord]*1e+15/box['delta'][coord]) * \ - 1e-15*box['delta'][coord] # rounding to 1e-15 of dimension - NodeCoords[node,coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros) - key[base[coord]] = "%.8e"%NodeCoords[node,coord] # translate position to string - if (key[base[coord]] == "%.8e"%box['min'][coord]): # compare to min of bounding box (i.e. is on outer face?) - Nmin += 1 # count outer (back) face membership - elif (key[base[coord]] == "%.8e"%box['max'][coord]): # compare to max of bounding box (i.e. is on outer face?) - Nmax += 1 # count outer (front) face membership - maxFlag[coord] = True # remember face membership (for linked nodes) + for node in range(Nnodes): + key = {} + maxFlag = [False, False, False] + Nmax = 0 + Nmin = 0 + for coord in range(3): # for each direction + if box['delta'][coord] != 0.0: + rounded = round(NodeCoords[node,coord]*1e+15/box['delta'][coord]) * \ + 1e-15*box['delta'][coord] # rounding to 1e-15 of dimension + NodeCoords[node,coord] = 0.0 if rounded == 0.0 else rounded # get rid of -0.0 (negative zeros) + key[base[coord]] = "%.8e"%NodeCoords[node,coord] # translate position to string + if (key[base[coord]] == "%.8e"%box['min'][coord]): # compare to min of bounding box (i.e. is on outer face?) + Nmin += 1 # count outer (back) face membership + elif (key[base[coord]] == "%.8e"%box['max'][coord]): # compare to max of bounding box (i.e. is on outer face?) + Nmax += 1 # count outer (front) face membership + maxFlag[coord] = True # remember face membership (for linked nodes) - if Nmin > 0: # node is on a back face - # prepare for any non-existing entries in the data structure - if key['x'] not in baseNode.keys(): - baseNode[key['x']] = {} - if key['y'] not in baseNode[key['x']].keys(): - baseNode[key['x']][key['y']] = {} - if key['z'] not in baseNode[key['x']][key['y']].keys(): - baseNode[key['x']][key['y']][key['z']] = 0 + if Nmin > 0: # node is on a back face + # prepare for any non-existing entries in the data structure + if key['x'] not in baseNode.keys(): + baseNode[key['x']] = {} + if key['y'] not in baseNode[key['x']].keys(): + baseNode[key['x']][key['y']] = {} + if key['z'] not in baseNode[key['x']][key['y']].keys(): + baseNode[key['x']][key['y']][key['z']] = 0 - baseNode[key['x']][key['y']][key['z']] = node+1 # remember the base node id + baseNode[key['x']][key['y']][key['z']] = node+1 # remember the base node id - if Nmax > 0 and Nmax >= Nmin: # node is on at least as many front than back faces - if any([maxFlag[i] and active[i] for i in range(3)]): - linkNodes.append({'id': node+1,'coord': NodeCoords[node], 'faceMember': [maxFlag[i] and active[i] for i in range(3)]}) + if Nmax > 0 and Nmax >= Nmin: # node is on at least as many front than back faces + if any([maxFlag[i] and active[i] for i in range(3)]): + linkNodes.append({'id':node+1,'coord':NodeCoords[node],'faceMember':[maxFlag[i] and active[i] for i in range(3)]}) - mfd_data[mfd_dict['entities']]['els'][0][0] += len(linkNodes) * 3 + mfd_data[mfd_dict['entities']]['els'][0][0] += len(linkNodes) * 3 - baseCorner = baseNode["%.8e"%box['min'][0]]["%.8e"%box['min'][1]]["%.8e"%box['min'][2]] # detect ultimate base node + baseCorner = baseNode["%.8e"%box['min'][0]]["%.8e"%box['min'][1]]["%.8e"%box['min'][2]] # detect ultimate base node - links = {'uid': 1705, 'label': 'links', 'els': [[7,0],[9,0]]} - linkID = 0 - for node in linkNodes: # loop over all linked nodes - linkCoord = [node['coord']] # start list of control node coords with my coords - for dir in range(3): # check for each direction - if node['faceMember'][dir]: # me on this front face - linkCoord[0][dir] = box['min'][dir] # project me onto rear face along dir - linkCoord.append(np.array(box['min'])) # append base corner - linkCoord[-1][dir] = box['max'][dir] # stretch it to corresponding control leg of "dir" + links = {'uid': 1705, 'label': 'links', 'els': [[7,0],[9,0]]} + linkID = 0 + for node in linkNodes: # loop over all linked nodes + linkCoord = [node['coord']] # start list of control node coords with my coords + for dir in range(3): # check for each direction + if node['faceMember'][dir]: # me on this front face + linkCoord[0][dir] = box['min'][dir] # project me onto rear face along dir + linkCoord.append(np.array(box['min'])) # append base corner + linkCoord[-1][dir] = box['max'][dir] # stretch it to corresponding control leg of "dir" - nLinks = len(linkCoord) - for dof in [1,2,3]: - tied_node = node['id'] - nterms = 1 + nLinks + nLinks = len(linkCoord) + for dof in [1,2,3]: + tied_node = node['id'] + nterms = 1 + nLinks - linkID += 1 - # Link header - links['els'].append('link{0}\n'.format(linkID)) - links['els'].append([linkID, 1]) - links['els'].append([0]) - links['els'].append([0]) - links['els'].append([0, 0, 0, tied_node]) + linkID += 1 + # Link header + links['els'].append('link{0}\n'.format(linkID)) + links['els'].append([linkID, 1]) + links['els'].append([0]) + links['els'].append([0]) + links['els'].append([0, 0, 0, tied_node]) - # these need to be put in groups of four - link_payload = [dof, 0, nterms] + # these need to be put in groups of four + link_payload = [dof, 0, nterms] - # Individual node contributions (node, dof, coef.) - for i in range(nterms): - if i == nLinks: - link_payload.append(baseCorner) - else: - link_payload.append(baseNode["%.8e"%linkCoord[i][0]]["%.8e"%linkCoord[i][1]]["%.8e"%linkCoord[i][2]]) - for i in range(nterms): - link_payload.append(dof) - for i in range(nterms): - if i == nLinks: - link_payload.append(1.0 - nLinks) - else: - link_payload.append(1.0) + # Individual node contributions (node, dof, coef.) + for i in range(nterms): + if i == nLinks: + link_payload.append(baseCorner) + else: + link_payload.append(baseNode["%.8e"%linkCoord[i][0]]["%.8e"%linkCoord[i][1]]["%.8e"%linkCoord[i][2]]) + for i in range(nterms): + link_payload.append(dof) + for i in range(nterms): + if i == nLinks: + link_payload.append(1.0 - nLinks) + else: + link_payload.append(1.0) - # Needs to be formatted 4 data points per row, character width of 20, so 80 total - for j in range(0, len(link_payload), 4): - links['els'].append(link_payload[j:j+4]) - if j+4 < len(link_payload): - links['els'].append(link_payload[j+4:]) + # Needs to be formatted 4 data points per row, character width of 20, so 80 total + for j in range(0, len(link_payload), 4): + links['els'].append(link_payload[j:j+4]) + if j+4 < len(link_payload): + links['els'].append(link_payload[j+4:]) - i = 0 - while i < len(mfd_data) and mfd_data[i]['uid'] < 1705: i += 1 + i = 0 + while i < len(mfd_data) and mfd_data[i]['uid'] < 1705: i += 1 - if mfd_data[i]['uid'] == 1705: del mfd_data[i] - mfd_data.insert(i, links) + if mfd_data[i]['uid'] == 1705: del mfd_data[i] + mfd_data.insert(i, links) #-------------------------------------------------------------------------------------------------- @@ -209,54 +209,54 @@ def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to parser = OptionParser(usage='%prog options [file[s]]', description = """ Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh. Use *py_connection to operate on model presently opened in MSC.Mentat. -""", version = scriptID) +""", version = script_id) parser.add_option('-p', '--port', - type = int, metavar = 'int', default = None, - help = 'Mentat connection port') + type = int, metavar = 'int', default = None, + help = 'Mentat connection port') parser.add_option('-x', - action = 'store_false', default = True, - help = 'no PBC along x direction') + action = 'store_false', default = True, + help = 'no PBC along x direction') parser.add_option('-y', - action = 'store_false', default = True, - help = 'no PBC along y direction') + action = 'store_false', default = True, + help = 'no PBC along y direction') parser.add_option('-z', - action = 'store_false', default = True, - help = 'no PBC along z direction') + action = 'store_false', default = True, + help = 'no PBC along z direction') (options, filenames) = parser.parse_args() remote = options.port is not None 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])) diff --git a/processing/mentat_spectralBox.py b/processing/mentat_spectralBox.py index 72206a8f4..de6307469 100755 --- a/processing/mentat_spectralBox.py +++ b/processing/mentat_spectralBox.py @@ -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)