| [e1a46d] | 1 | #!@PYTHON@
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| 2 | #
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| 3 | # Create the steps from bcc to fcc
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| 4 | #
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| 5 | # Note: PCP config file should contain two configurations which are linearly interpolated in the given amount of steps
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| 6 |
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| 7 | import sys, string, re, math, os
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| 8 | wrerr = sys.stderr.write
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| 9 |
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| 10 | if len(sys.argv) < 3:
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| 11 | wrerr("Usage: "+sys.argv[0]+" <config> <steps>\n")
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| 12 | sys.exit(1)
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| 13 |
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| 14 | config = open(sys.argv[1], "r")
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| 15 | steps = int(sys.argv[2])
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| 16 |
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| 17 | # find the lines where source and target configuration start
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| 18 | nr=0
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| 19 | source=0
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| 20 | target=0
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| 21 | box=0
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| 22 | boxlength = []
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| 23 | for line in config:
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| 24 | nr=nr+1
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| 25 | if re.compile("BoxLength").match(line):
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| 26 | box=nr
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| 27 | if box != 0 and nr > box and nr < box+4:
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| 28 | numbers = line.split()
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| 29 | for j in range(len(numbers)):
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| 30 | boxlength.append(float(numbers[j]))
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| 31 | if re.compile("Ion_Type[0-9]+[_]+").match(line) and source == 0:
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| 32 | source=nr
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| 33 | if "# ====== MD step" in line:
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| 34 | target=nr+1
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| 35 | if target == 0:
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| 36 | wrerr("Could find only a single geometry, need at least two!\n")
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| 37 | sys.exit(1)
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| 38 | print "Changing from config starting at line %d to the one starting at line %d ..." % (source, target)
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| 39 |
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| 40 | #for i in range(len(boxlength)):
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| 41 | # print "%lg\t" % (boxlength[i])
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| 42 | # parse the source configuration
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| 43 | config.seek(0)
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| 44 | n=0
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| 45 | nr=0
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| 46 | sourcepos = []
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| 47 | sourcemax = [0., 0., 0.]
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| 48 | for line in config:
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| 49 | nr=nr+1
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| 50 | if source > nr:
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| 51 | continue
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| 52 | else:
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| 53 | if re.compile("Ion_Type[0-9]+[_]+").match(line):
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| 54 | words = line.split()
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| 55 | print words
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| 56 | sourcepos.append(words[0]+"="+words[1]+"="+words[2]+"="+words[3])
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| 57 | for j in range(3):
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| 58 | if sourcemax[j] < float(words[j+1]):
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| 59 | sourcemax[j] = float(words[j+1])
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| 60 | n=n+1
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| 61 | else:
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| 62 | if "#" in line: # we break on the next comment line after source
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| 63 | break
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| 64 | print "I found ",n," atoms in source config."
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| 65 |
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| 66 | # parse the target configuration
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| 67 | config.seek(0)
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| 68 | n=0
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| 69 | nr=0
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| 70 | targetpos = []
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| 71 | targetmax= [0., 0., 0.]
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| 72 | for line in config:
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| 73 | nr=nr+1
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| 74 | if target > nr:
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| 75 | continue
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| 76 | else:
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| 77 | if re.compile("Ion_Type[0-9]+[_]+").match(line):
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| 78 | words = line.split()
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| 79 | print words
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| 80 | targetpos.append(words[0]+"="+words[1]+"="+words[2]+"="+words[3])
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| 81 | for j in range(3):
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| 82 | if targetmax[j] < float(words[j+1]):
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| 83 | targetmax[j] = float(words[j+1])
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| 84 | n=n+1
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| 85 | else:
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| 86 | if "#" in line: # we break on the next comment line after source
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| 87 | break
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| 88 | print "I found ",n," atoms in target config."
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| 89 | targetmax[2] = 2.64357
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| 90 | # Now as we have the two configs, we need go through the steps desired and write the output files
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| 91 | diff = [0., 0., 0.]
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| 92 | BoxLength = [0., 0., 0., 0., 0., 0.]
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| 93 | for i in range(steps+1):
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| 94 | # change the boxlength
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| 95 | if i == 0:
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| 96 | for j in range(6):
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| 97 | BoxLength[j] = boxlength[j]
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| 98 | else:
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| 99 | BoxLength[0] = boxlength[0] + boxlength[0]*(targetmax[0]/sourcemax[0]-1.)*(float(i)/float(steps))
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| 100 | BoxLength[1] = boxlength[1] + boxlength[1]*(targetmax[0]/sourcemax[0]-1.)*(float(i)/float(steps))
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| 101 | BoxLength[2] = boxlength[2] + boxlength[2]*(targetmax[1]/sourcemax[1]-1.)*(float(i)/float(steps))
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| 102 | BoxLength[3] = boxlength[3] + boxlength[3]*(targetmax[0]/sourcemax[0]-1.)*(float(i)/float(steps))
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| 103 | BoxLength[4] = boxlength[4] + boxlength[4]*(targetmax[0]/sourcemax[0]-1.)*(float(i)/float(steps))
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| 104 | BoxLength[5] = boxlength[5] + boxlength[5]*(targetmax[2]/sourcemax[2]-1.)*(float(i)/float(steps))
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| 105 | # write the initial config file to the new destination
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| 106 | newdir="step%02d" % (i)
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| 107 | if not os.path.isdir(newdir):
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| 108 | if os.path.isfile(newdir):
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| 109 | raise OSError("a file with the same name as the desired " \
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| 110 | "dir, '%s', already exists." % newdir)
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| 111 | else:
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| 112 | os.mkdir(newdir)
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| 113 | output = file("step%02d/%s" % (i,sys.argv[1]),"w")
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| 114 | config.seek(0)
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| 115 | nr=0
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| 116 | for line in config:
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| 117 | nr=nr+1
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| 118 | if box < nr and box+4 > nr:
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| 119 | j=nr-box-1
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| 120 | for m in range(j+1):
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| 121 | if j==2:
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| 122 | j=j+1
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| 123 | output.write("%lg\t" % (BoxLength[j+m]))
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| 124 | else:
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| 125 | output.write("%lg\t" % (BoxLength[j+m]))
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| 126 | output.write("\n")
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| 127 | continue
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| 128 | output.write(line)
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| 129 | if source <= nr+1:
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| 130 | break
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| 131 | # add the shifted coordinates
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| 132 | for j in range(n):
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| 133 | sourceatoms = sourcepos[j].split("=")
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| 134 | targetatoms = targetpos[j].split("=")
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| 135 | for m in range(3):
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| 136 | diff[m] = (float(targetatoms[m+1])-float(sourceatoms[m+1]))*float(i)/float(steps)
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| 137 | output.write("%s\t%2.10f\t%2.10f\t%2.10f\t#\n" % (sourceatoms[0], float(sourceatoms[1])+diff[0], float(sourceatoms[2])+diff[1], float(sourceatoms[3])+diff[2]))
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| 138 | output.close()
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| 139 | config.close()
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