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nim-hrkn edited this page Nov 9, 2016
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Welcome to the find_wy wiki!
TSPACE web site is http://aquarius.mp.es.osaka-u.ac.jp/~tspace/
tsp98.f and prmtsp.f are necessary.
git clone git@github.com:nim-hrkn/m_tspace.git.
Note
- . You must make the same compiler as that used in m_tspace.
- . 'ifort -assume realloc_lhs' if you use ifort.
./find_wy cif_sample/input_y2co17.txt
- .原子数が多い場合はrandom searchを行う。（defaultでは最大1000回）
- .原子数が少ない場合は全探索して一つ選択する。
nspecies 2 species_name Si O species_num 4 8 spacegroup 143 originchoice 1 a 10. b 11. c 12. cosa 0 cosb 0 cosc 0 #selectone true ! true|false OBSOLETE randomseed auto ! auto|integer , autoはclockからrandomseedを作成 latinfo_only false ! false|true <-- LAT.jsonを出力して終了。
格子の情報だけを得たい場合は
latinfo_only true
その他の情報も得たい場合は
latinfo_only false
として呼ぶ。
Note that they accepts python2 and python3.
library = find_wy.py
You must set the FIND_WY enviromental variable to call find_wy, e.g.,
$ export FIND_WY=/home/kino/tmp/test_env/find_wy/find_wy
fw=find_wy.find_wy(143) # <--- Change this number if you want to use another spacegroup
lat=fw.lat_info()
print lat
#set seed if you want to make the same series of random numbers to make lat
seed=100
np.random.seed(seed)
a,b,c,alpha,beta,gamma = set_lat(lat)
species_name=["Si", "O"] # <--- YOu must define.
species_num=[4, 8] # <--- you must define
print a,b,c,alpha,beta,gamma,species_name,species_num
rskel,r=fw.get_positions( a,b,c,alpha,beta,gamma,species_name,species_num ,randomseed=seed)
print rskel
print r
$ ./py/find_wy_main.py
\rm -rf /home/kino/tmp/test_env/find_wy/execc78691385d3b2569c3a600fab7527450
{u'a': u'0', u'c': u'0', u'b': u'a', u'beta': 90, u'gamma': 60, u'spacegroupid': 143, u'alpha': 90, u'Z': 1, u'originchoide': 1}
5.43404941791 5.43404941791 3.34043262113 90 90 60 ['Si', 'O'] [4, 8]
['species_num 4 8 \n', 'species_name Si O \n', 'cosb 6.12323399574e-17 \n', 'cosa 6.12323399574e-17 \n', 'orginchoice 1 \n', 'cosc 0.5 \n', 'a 5.43404941791 \n', 'c 3.34043262113 \n', 'b 5.43404941791 \n', 'randomseed 100 \n', 'nspecies 2 \n', 'spacegroup 143 \n']
\rm -rf /home/kino/tmp/test_env/find_wy/exec5404688f55d9111fcf55786a30212279
{u'spacegroupid': 143, u'lat': [5.43404941791, 5.43404941791, 3.34043262113, 90.0, 90.0, 120.0], u'atoms': [{u'name': u'Si', u'num_uniqvar': 1, u'add': [0.0, 0.0, 0.0], u'mul': 1, u'wy': u'a', u'xyzch': [u'0', u'0', u'z']}, {u'name': u'Si', u'num_uniqvar': 3, u'add': [0.0, 0.0, 0.0], u'mul': 3, u'wy': u'd', u'xyzch': [u'x', u'y', u'z']}, {u'name': u'O', u'num_uniqvar': 1, u'add': [0.333333333333333, 0.666666666666667, 0.0], u'mul': 1, u'wy': u'b', u'xyzch': [u'0', u'0', u'z']}, {u'name': u'O', u'num_uniqvar': 3, u'add': [0.0, 0.0, 0.0], u'mul': 3, u'wy': u'd', u'xyzch': [u'x', u'y', u'z']}, {u'name': u'O', u'num_uniqvar': 1, u'add': [0.0, 0.0, 0.0], u'mul': 1, u'wy': u'a', u'xyzch': [u'0', u'0', u'z']}, {u'name': u'O', u'num_uniqvar': 3, u'add': [0.0, 0.0, 0.0], u'mul': 3, u'wy': u'd', u'xyzch': [u'x', u'y', u'z']}], u'originchoice': 1}
{u'spacegroupid': 143, u'lat': [5.43404941791, 5.43404941791, 3.34043262113, 90.0, 90.0, 120.0], u'atoms': [{u'num_uniqvar': 1, u'mul': 1, u'frac': [0.0, 0.0, 0.04971772349719251], u'name': u'Si', u'wy': u'a'}, {u'num_uniqvar': 3, u'mul': 3, u'frac': [0.908189377373128, 0.09765859753870422, 0.04031338096905369], u'name': u'Si', u'wy': u'd'}, {u'num_uniqvar': 1, u'mul': 1, u'frac': [0.333333333333333, 0.666666666666667, 0.92645174765419], u'name': u'O', u'wy': u'b'}, {u'num_uniqvar': 3, u'mul': 3, u'frac': [0.07564077406631106, 0.911789607956127, 0.09182217661518818], u'name': u'O', u'wy': u'd'}, {u'num_uniqvar': 1, u'mul': 1, u'frac': [0.0, 0.0, 0.121077706707457], u'name': u'O', u'wy': u'a'}, {u'num_uniqvar': 3, u'mul': 3, u'frac': [0.994574503292715, 0.778250349290332, 0.01966502222769279], u'name': u'O', u'wy': u'd'}], u'originchoice': 1}
First run find_wy to have the file, POS_WY_SKEL.json
$ ./py/read_pos_wy_skel.py POS_WY_SKEL.json original description Si [u'0', u'0', u'z'] [0.0, 0.0, 0.0] Si [u'0', u'0', u'z'] [0.333333333333333, 0.666666666666667, 0.0] Si [u'0', u'0', u'z'] [0.666666666666667, 0.333333333333333, 0.0] Si [u'0', u'0', u'z'] [0.666666666666667, 0.333333333333333, 0.0] O [u'0', u'0', u'z'] [0.0, 0.0, 0.0] O [u'0', u'0', u'z'] [0.666666666666667, 0.333333333333333, 0.0] O [u'0', u'0', u'z'] [0.0, 0.0, 0.0] O [u'0', u'0', u'z'] [0.666666666666667, 0.333333333333333, 0.0] O [u'0', u'0', u'z'] [0.333333333333333, 0.666666666666667, 0.0] O [u'x', u'y', u'z'] [0.0, 0.0, 0.0] conversion Si [ 0. 0. 0.88327668] Si [ 0.33333333 0.66666667 0.89893586] Si [ 0.66666667 0.33333333 0.03264738] Si [ 0.66666667 0.33333333 0.4249024 ] O [ 0. 0. 0.51770598] O [ 0.66666667 0.33333333 0.63373223] O [ 0. 0. 0.90542048] O [ 0.66666667 0.33333333 0.03209262] O [ 0.33333333 0.66666667 0.27208314] O [ 0.78311704 0.66579814 0.37302571]
$ ./py/ase_crystal_from_json.py POS_WY.json summary Si [ 2.96008865e-16 5.12702393e-16 4.83419162e+00] Si [ -3.24826161e-15 5.77350269e+00 4.97207966e+00] Si [ 5. 2.88675135 1.27286323] Si [ 5. 2.88675135 0.70980008] O [ 6.80319089e-16 1.17834723e-15 1.11104539e+01] O [ 5. 2.88675135 5.68814455] O [ 5.46793586e-16 9.47074273e-16 8.92981693e+00] O [ 5. 2.88675135 6.47742627] O [ -3.11272013e-15 5.77350269e+00 7.18564001e+00] O [ -4.74573897 8.31062624 10.69527758] O [ 0.17565605 0.39501041 10.69527758] O [ 4.57008293 8.61487143 10.69527758] POSCAR.ase is made. for vasp POS.new.json is made. for json
$ ./py/crystal_from_pos_wy_skel_all.py POS_WY_SKEL_ALL.json POSCAR.new is made.It reads POS_WY_SKEL_ALL.json, which is one of the output files of find_wy, and supply (x,y,z) to give numerical coordinates.