终端同步

VASP.py

@@ -93,7 +93,7 @@ def read_poscar(file_name):
 
 
 def write_poscar(file_name, lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, coordinates, selective):
-    with open(file_name) as output_file:
+    with open(file_name, 'w') as output_file:
         description = ""
         for atom in elements:
             description += "%s  " % atom
@@ -113,8 +113,13 @@ def write_poscar(file_name, lattice, basis, elements, num_atoms, selectiveflag,
         if re.search(r'^[Dd]', coordinate_type):
             coordinates = kardir(basis, coordinates)
 
+        # keeping dimension the same
+        if len(coordinates) - len(selective) > 0:
+            for i in xrange(len(selective), len(coordinates)):
+                selective.append(['', '', ''])
+
         for i in xrange(0, len(coordinates)):
-            output_file.write("%16.10f  %16.10f  %16.10f %s %s %s" % (coordinates[i][0], coordinates[i][1], coordinates[i][2],
+            output_file.write("%16.10f  %16.10f  %16.10f %s %s %s\n" % (coordinates[i][0], coordinates[i][1], coordinates[i][2],
                                                                       selective[i][0], selective[i][1], selective[i][2]))
 
 

cluster.py

@@ -0,0 +1,100 @@
+#!/bin/env python
+
+import sys
+from VASP import read_poscar
+from VASP import write_poscar
+
+pos=[    [5.8542326628848222, 8.6627288616639202, 5.8614577958952649],
+ [19.1457883626720999,  8.6618038283281429, 5.8617364474046472],
+ [12.4996292966500064, 15.5432216444165245, 5.8505835915867426],
+ [12.4996643651611539, 20.1731884887187114, 5.8689022630647800],
+ [ 9.8642435232315151, 10.9792336123257641, 5.8473985708617429],
+ [15.1357647669649271, 10.9791445570918995, 5.8472893749556079],
+ [ 8.5184517876025279, 17.9094319106692339, 5.8404122824553175],
+ [16.4803808630984250, 17.9094750385708004, 5.8387698865076327],
+ [ 5.8239686065138274, 13.2430151734748378, 5.8366213458278002],
+ [19.1756365833384415, 13.2430391136603038, 5.8350835858967098],
+ [ 9.8067481495349647,  6.3495826586473152, 5.8328105220657820],
+ [15.1937500782213348,  6.3490794563218671, 5.8330243464332350],
+ [ 7.1904979234005300, 15.5651383106483276, 5.8259475258861704],
+ [17.8087338711519259, 15.5652572833824330, 5.8245572976908671],
+ [12.5000405878065539,  6.3729308348105809, 5.8218156883507675],
+ [ 9.8820227202533282, 20.1615823696097038, 5.7844099681486449],
+ [15.1170850426095829, 20.1616169957727216, 5.7828276269297225],
+ [ 9.8122233556618639, 15.6062771111702467, 5.7978947497764279],
+ [15.1870343137687520, 15.6062640823243584, 5.7973780728100950],
+ [ 8.4652256331715456, 13.2749294624138567, 5.7971824780871497],
+ [16.5343455597751188, 13.2747877636130056, 5.7962617201112181],
+ [11.1535516011113938,  8.6216877683269875, 5.7938944716497121],
+ [13.8466676349981466,  8.6214440419079121, 5.7943806235593751],
+ [11.1490651429739547, 17.9761055906219411, 5.7801712196507227],
+ [13.8496966421608665, 17.9760454193992452, 5.7804718311372252],
+ [ 7.0806236588204898, 10.9316354119090882, 5.7771740040302655],
+ [17.9196297301407306, 10.9312779304740122, 5.7762362324898824],
+ [11.1466749444189528, 13.2819533837950718, 5.7838345774454654],
+ [13.8529870474015446, 13.2820766532686125, 5.7835474481279379],
+ [ 8.4321768825083225,  8.5939250693677529, 5.7740131122559575],
+ [16.5679980292057039,  8.5938416892026712, 5.7741364855875670],
+ [12.5001416610547142, 10.9397393077747278, 5.7828449293659103],
+ [ 4.5545882618995801, 10.9372558294256201, 5.7785902068256227],
+ [20.4451384058851815, 10.9363239532347656, 5.7776259828189218],
+ [ 7.1740910330408996,  6.4035538749654872, 5.7743942607092302],
+ [17.8255437064344839,  6.4026847899577053, 5.7752304099191845],
+ [ 5.8568607540469744, 11.7651243950267137, 3.6608883120443871],
+ [19.1436939971528197, 11.7667770355312129, 3.6604706101656226],
+ [ 8.5426819733447310,  7.1162155758867005, 3.6587428673277396],
+ [16.4586851339770135,  7.1174272612378884, 3.6584426541561030],
+ [ 9.8136168292230721, 18.6222830403632145, 3.6663636877511325],
+ [12.4995145412520650, 18.6312555181673005, 3.6548235558601054],
+ [15.1831458084883888, 18.6231885937048105, 3.6654539879666501],
+ [ 7.1905459875948967,  9.4375562195163099, 3.6484179628325952],
+ [17.8089055071839013,  9.4369088439504623, 3.6479812702380898],
+ [ 8.5106357931706622, 16.3341139136295936, 3.6206149773764928],
+ [16.4878788265676661, 16.3351489370489098, 3.6202856639716825],
+ [ 7.1851154172870926, 14.0394083936080634, 3.6189915219198379],
+ [17.8144949861972179, 14.0402357499072128, 3.6176999795794704],
+ [11.1752410014319725,  7.1318705445070725, 3.6144877158625528],
+ [13.8259816450236723,  7.1317412695549667, 3.6160137060298552],
+ [12.4996158325251283, 14.0602012265637786, 3.6075313553575503],
+ [11.1505765206244050, 11.7223267224017249, 3.6068877754449300],
+ [13.8502987706658622, 11.7232173727088629, 3.6066155977606549],
+ [11.1498571077593756, 16.4113638209514292, 3.5760358823059648],
+ [13.8485674418494789, 16.4107606851385235, 3.5759996716579900],
+ [ 9.7891812762153094,  9.3780459876955025, 3.5711816461132022],
+ [15.2101276867227853,  9.3789002597240856, 3.5716568501771477],
+ [ 8.4393762279991158, 11.7162332293038247, 3.5731022570868047],
+ [16.5617228908786025, 11.7167625758915364, 3.5727113095524476],
+ [ 9.7777043270454023, 14.0726331225701404, 3.5575765222356122],
+ [15.2221258811660487, 14.0731293508385509, 3.5569787180677124],
+ [12.5002525096445680,  9.3601828303336774, 3.5542392678181502],
+ [ 8.5320020693175405, 14.7910868434451501, 1.5187845488341576],
+ [16.4668862744892053, 14.7933338472709952, 1.5180927858648652],
+ [ 9.8887961265038822, 17.1463588545972883, 1.5146754477426800],
+ [15.1081461908212749, 17.1487848478586997, 1.5146578136720801],
+ [12.5020410432031692,  7.9226726991187002, 1.5145458408523949],
+ [ 7.1705177122920194, 12.4396711855405453, 1.5118473503168626],
+ [17.8294570832127093, 12.4413426726000420, 1.5111017865561325],
+ [ 9.7860910857492662,  7.9205963993608606, 1.5076994932664651],
+ [15.2171821019143749,  7.9212608271536356, 1.5081308582786375],
+ [12.5003167921428595, 12.5030053504844716, 1.4977462763204274],
+ [12.4991949683432502, 17.0771780327954161, 1.4738220963398374],
+ [11.1387551669516434, 14.8215426119312426, 1.4782594263777826],
+ [13.8601305439163998, 14.8216561851532873, 1.4781982275442249],
+ [ 9.8121148532213063, 12.5195525373460228, 1.4769349629129875],
+ [15.1895751883270265, 12.5200970496508468, 1.4764890499645225],
+ [11.1714269060458786, 10.1654087289077619, 1.4752615333521850],
+ [13.8288820354799782, 10.1668810853471037, 1.4752820024869751],
+ [ 8.5369568562395006, 10.2155217644163354, 1.4700324542918575],
+ [16.4634057452755975, 10.2154701580726197, 1.4701338323750650]
+]
+
+
+lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, coordinates, selective = read_poscar(sys.argv[1])
+
+temp = coordinates[:119]
+temp.extend(pos)
+temp.extend(coordinates[119:])
+num_atoms[0] += 82
+
+write_poscar('POSCAR.vasp', lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, temp, selective)
+

flagck.py

@@ -3,7 +3,6 @@
 import re
 
 file_name = 'POSCAR'
-
 with open(file_name) as input_file:
     content = input_file.readlines()
 
@@ -15,14 +14,13 @@
 print "------------------------------------------"
 for i in xrange(9, len(content)):
     temp = pattern.split(content[i].strip())
-    length = len(temp)
 
-    if length == 1:
+    if len(temp) == 1:
         exit(0)
 
-    if length != 6:
+    if len(temp) != 6:
         print "-----------"
-        print "%4d:    %s" % (i - 8, content[i].strip())
+        print "%4d:    %s" % (i - 8, content[i].rstrip())
         print "-----------"
         continue
 
@@ -36,8 +34,8 @@
         continue
     else:
         pre_flag = flag
-        print "%4d:    %s" % (i - 9, content[i - 1].strip())
-        print "%4d:    %s" % (i - 8, content[i].strip())
+        print "%4d:    %s" % (i - 9, content[i - 1].rstrip())
+        print "%4d:    %s" % (i - 8, content[i].rstrip())
         print "-----------"
 
 print ""

hlcluster.py

@@ -0,0 +1,157 @@
+#!/bin/env python
+
+import sys
+import VASP
+import re
+pos1 = [[  8.52663112, 14.79337948, 14.52301881],
+      [ 16.47997580, 14.79343097, 14.51908835],
+      [ 11.14789630, 14.85687226, 14.51622011],
+      [ 13.85760488, 14.85722967, 14.51548506],
+      [  9.78287211, 12.49254211, 14.51553649],
+      [ 15.22261961, 12.49238169, 14.51371286],
+      [ 11.13563815, 10.14933498, 14.51532174],
+      [ 13.86597088, 10.14847010, 14.51428049],
+      [ 12.50012880,  7.90943392, 14.51976956],
+      [ 12.50372460, 12.50075283, 14.72163059],
+      [  9.78440676, 17.09766453, 14.48773211],
+      [ 15.22295554, 17.09739644, 14.48602752],
+      [  7.15981020, 12.55477124, 14.48660210],
+      [ 17.84482988, 12.55353408, 14.48367771],
+      [ 12.50374400, 17.08727980, 14.47394451],
+      [  9.87605186,  7.84598863, 14.48403817],
+      [ 15.12400216,  7.84505696, 14.48361730],
+      [  8.52637045, 10.20520181, 14.47173998],
+      [ 16.47553419, 10.20431563, 14.47057725],
+      [ 12.50162082, 15.62744811, 12.44805426],
+      [  9.78981284, 10.93427811, 12.44606936],
+      [ 15.21142132, 10.93350182, 12.44513778],
+      [  9.80328010, 15.61779801, 12.45193423],
+      [ 15.19879468, 15.61737840, 12.45016375],
+      [  8.44957785, 13.27629042, 12.45064043],
+      [ 16.55283128, 13.27448455, 12.44803144],
+      [ 11.14706080,  8.60486927, 12.44908613],
+      [ 13.85249392,  8.60483110, 12.44875320],
+      [ 11.14080909, 13.28417801, 12.37402178],
+      [ 13.86129087, 13.28384618, 12.37357051],
+      [ 12.50040244, 10.93013268, 12.37344562],
+      [ 11.16790993, 17.86382119, 12.37953773],
+      [ 13.83623659, 17.86393157, 12.37839810],
+      [  7.18532081, 10.97162350, 12.37640674],
+      [ 17.81618039, 10.96917629, 12.37482430],
+      [  8.52043182,  8.66069151, 12.37565154],
+      [ 16.47890651,  8.65897510, 12.37489045],
+      [  7.19477108, 15.56239596, 12.31904726],
+      [ 17.80774841, 15.56122995, 12.31656077],
+      [ 12.49966163,  6.37471536, 12.31590153],
+      [  8.55158958, 17.88809068, 12.32062468],
+      [ 16.45265851, 17.88723731, 12.31870385],
+      [  5.85767123, 13.22339656, 12.31734762],
+      [ 19.14459556, 13.22189528, 12.31494919],
+      [  9.80713808,  6.38527824, 12.31505608],
+      [ 15.19009880,  6.38373013, 12.31477027],
+      [  7.17419958, 18.59601593, 10.22637496],
+      [ 17.82830097, 18.59530226, 10.22321914],
+      [  4.55461164, 14.05906469, 10.22249110],
+      [ 20.44650799, 14.05754717, 10.21944311],
+      [  8.42136455, 16.41006373, 10.18936218],
+      [ 16.58069447, 16.40942145, 10.18738731],
+      [ 12.50057691, 14.05937074, 10.21535316],
+      [  9.87962931,  4.83952796, 10.21780715],
+      [ 15.11771081,  4.83864890, 10.21828204],
+      [ 11.14849921, 11.71880557, 10.21433043],
+      [ 13.85197245, 11.71839398, 10.21388722],
+      [  7.07163033, 14.07557769, 10.18966559],
+      [ 17.92981245, 14.07451466, 10.18715058],
+      [ 11.15032078,  7.01258145, 10.18585555],
+      [ 13.84805427,  7.01260553, 10.18468742],
+      [ 11.15374139, 16.38258017, 10.19406419],
+      [ 13.84797712, 16.38262181, 10.19305577],
+      [  8.46142283, 11.72200026, 10.19193337],
+      [ 16.53912952, 11.72137050, 10.19082751],
+      [  9.80868275,  9.39175408, 10.19042848],
+      [ 15.19121513,  9.39139801, 10.19000713],
+      [ 12.50135228, 18.62698462, 10.16962569],
+      [  7.19030646,  9.43427206, 10.16393883],
+      [ 17.80928245,  9.43264096, 10.16320550],
+      [  9.81079791, 18.65246946, 10.15161108],
+      [ 15.19173033, 18.65258132, 10.15047131],
+      [  5.82378702, 11.74973673, 10.14719363],
+      [ 19.17687861, 11.74901365, 10.14552497],
+      [  8.51399694,  7.09243078, 10.14437820],
+      [ 16.48462386,  7.09196221, 10.14483167],
+      [  9.86853781, 14.01808792, 10.15838631],
+      [ 15.13244188, 14.01737556, 10.15760583],
+      [ 12.49981106,  9.46102591, 10.15664749],
+      [  5.85053309, 16.33653652, 10.14074533],
+      [ 19.15069695, 16.33600992, 10.13783351],
+      [ 12.49931777,  4.82427576, 10.13718242],
+      [  7.18523207, 17.13677427,  8.01539152],
+      [ 17.81493362, 17.13612020,  8.01291170],
+      [  5.82590638, 14.78219838,  8.01390731],
+      [ 19.17465308, 14.78132898,  8.01158728],
+      [ 11.14006478,  5.58027740,  8.01015883],
+      [ 13.85860959,  5.58043958,  8.00916219],
+      [  8.53147710, 19.37002966,  8.00455541],
+      [ 16.46920527, 19.36960314,  8.00259121],
+      [  8.46738535, 14.82637476,  8.00658441],
+      [ 16.53288730, 14.82600301,  8.00537653],
+      [ 11.13861128, 14.84751514,  8.00240172],
+      [ 13.86148623, 14.84720046,  8.00199886],
+      [ 12.49994745, 12.50006125,  8.00063110],
+      [  9.78416859, 17.21308386,  7.99515119],
+      [ 15.21588849, 17.21290637,  7.99420108],
+      [  4.56377466, 12.49940921,  7.99904840],
+      [ 20.43610028, 12.49779898,  7.99698832],
+      [ 12.49920704,  7.84559494,  8.00242003],
+      [  7.05812000, 12.49413290,  7.99278396],
+      [ 17.94178450, 12.49358184,  7.99141504],
+      [  9.78582520, 12.50421909,  8.00089516],
+      [ 15.21413615, 12.50369827,  8.00052122],
+      [ 12.50007180, 17.15587369,  7.99900446],
+      [ 11.14649591, 10.14802062,  7.99941063],
+      [ 13.85314391, 10.14774254,  7.99948145],
+      [  9.77481016,  7.79245421,  7.98959054],
+      [ 15.22469429,  7.79201704,  7.98943559],
+      [  8.46632515, 10.17202968,  7.99540983],
+      [  8.53256540,  5.62907836,  7.99458204],
+      [ 16.46612157,  5.62801086,  7.99582303],
+      [ 16.53337285, 10.17092209,  7.99467923],
+      [ 11.13544681, 19.42130452,  7.97773530],
+      [ 13.86508896, 19.42136867,  7.97785955],
+      [  5.82074273, 10.21941636,  7.97126648],
+      [ 19.17882835, 10.21844766,  7.97010409],
+      [  7.18631774,  7.85639597,  7.96997322],
+      [ 17.81284174,  7.85499234,  7.97028496]]
+
+# hlcluster.py inputfile.gjf -n +n n-n
+
+lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, coordinates, selective = VASP.read_poscar('POSCAR')
+with open(sys.argv[1]) as IN:
+    input_file = IN.readlines()
+    space = re.compile(r'\s+')
+    a = int(sys.argv[2]) - 1
+    b = int(sys.argv[3]) - 1
+    temp = sys.argv[4].split('-')
+    c = int(temp[0]) - 1
+    d = int(temp[1])
+
+    gjfcoord = []
+    for i in xrange(5, len(input_file)):
+        if input_file[i].strip() == '':
+            break
+        line = space.split(input_file[i].strip())
+        gjfcoord.append([float(line[1]), float(line[2]), float(line[3])])
+
+    coor = []
+    num_atoms[2] = 0
+    for i in xrange(c, d):
+        v1 = gjfcoord[i][0] - gjfcoord[a][0] + pos1[b][0]
+        v2 = gjfcoord[i][1] - gjfcoord[a][1] + pos1[b][1]
+        v3 = gjfcoord[i][2] - gjfcoord[a][2] + pos1[b][2]
+        pos1.append([v1, v2, v3])
+        num_atoms[2] += 1
+    num_atoms[2] -= 2
+
+VASP.write_poscar('POSCAR.vasp', lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, pos1, selective)
+
+

imagefreq.py

@@ -2,7 +2,7 @@
 
 import re
 from VASP import read_total_atoms
-from VASP import grep_OUTCAR
+from VASP import grep_outcar
 
 print ""
 print "    --------------------Processing--------------------"
@@ -12,7 +12,7 @@
 atom_num += 2
 
 string = "grep \"f/i\" OUTCAR -A %d" % atom_num
-content = grep_OUTCAR(string)
+content = grep_outcar(string)
 
 pattern = re.compile("([0-9]+)\s+f/i")
 content_length = len(content)