crystal code with lc-blyp functional

crystal is a computational tool for solid state chemistry and physics. Basically, it does DFT. I post here an example of lc-blyp calculation of bulk water system.

When I did the lc-blyp calculation, the scf not converge is a problem. So I did a blyp calculation first. Then copy the fort.9 file to a new folder of fort.20 which is the density matrix file. And I will add a GUESSP command to the INPUT for lc-blyp calculation.

Here is the inputs:

INPUT for blyp calculation

Water cube
CRYSTAL
0 0 0
1
11.8172 11.8172 11.8172 90. 90. 90.
165
8 0.966182090512 1.00021468707 1.4854507836
8 1.03919930271 1.40081195207 1.57239938395
8 1.2300162475 0.527247909826 1.33289637139
8 0.768640540906 1.65014267339 1.3298380327
8 1.15689283417 1.2052291575 1.08481399993
8 0.903492451681 1.21632146363 1.38370900044
8 0.762101766916 0.505654892868 0.887620671563
8 1.38305427682 0.459265985174 1.53107572014
8 1.50650348644 0.456861016146 1.17375080391
8 0.63803650611 1.15520588634 0.658485597265
8 1.45252310192 1.04503698 1.09088574282
8 0.446270182446 0.842531479538 0.927859729885
8 1.43138112243 0.708681921267 0.740832092205
8 0.937938767221 1.03809015672 0.702070372
8 0.863986223471 1.24494550316 0.67097527333
8 1.26616296585 0.550525843685 0.700526097553
8 0.808251954778 1.01392546458 0.888978438209
8 0.700633060285 1.30514241952 1.36784449785
8 1.27978945943 1.22268439224 1.87452839928
8 0.61985597265 1.42719138205 1.54634253461
8 1.52579096571 0.709874674204 0.49502242494
8 0.984720576786 0.61250702366 2.05818366449
8 0.900647784585 0.474448261856 1.22569508852
8 1.49653835088 1.28823308398 0.830222810818
8 1.79160029449 1.07211158312 1.2086718512
8 1.83282960431 0.803301205023 0.9671824967
8 1.34537504654 0.873155146735 1.24777189182
8 0.4377635142 1.24948481874 1.26121712419
8 1.61083522323 0.963454117727 1.32491478523
8 0.89343812409 0.582376366652 1.52855871103
8 0.492430694242 1.0714599059 0.497475290255
8 1.32287047693 1.24018718478 1.48182623633
8 1.08089682835 0.710079629692 1.69978937481
8 0.566233625563 1.66400610974 1.25198558034
8 0.188996462783 0.885536929222 1.46524041228
8 0.92452552212 1.23048649426 1.03169295603
8 0.617660274854 0.817834258538 1.08969459771
8 1.33952662221 0.537026114477 0.97252276343
8 1.21163067393 1.07015274346 0.705801289646
8 0.708953559219 1.40961251396 1.10277104559
8 1.06568992655 0.706494854957 0.400919507159
8 1.12978751312 0.876184290695 0.910686033917
8 1.55138340724 1.51283019666 1.84138306875
8 0.943388281488 0.379874928071 0.842503892631
8 1.35594709407 0.919504451139 1.62474444031
8 0.948775175168 0.840589733609 1.20458492706
8 0.622394898961 1.20107174288 1.02580848255
8 0.784972836205 0.848350032157 1.42938403344
8 1.08217014183 0.360261737129 1.27039222489
8 1.16518735403 1.41018464611 0.848232999357
8 0.851257319839 0.708795315303 0.771359374471
8 0.682134261923 0.819043512846 1.64355321057
8 1.15068908032 0.962640642453 1.15036303016
8 0.595814321497 0.971598517415 0.797778153877
8 1.22474054768 0.674640862472 1.14489794537
1 1.04184933825 0.980869495312 1.46944707714
1 0.966587770369 1.07866017331 1.46048801747
1 1.00937303253 1.3425173476 1.52038587821
1 0.996500440037 1.36528094642 1.63609315235
1 1.19357995126 0.452229885252 1.3260631114
1 1.2984623261 0.518463849304 1.38540804928
1 0.69602291575 1.63709626646 1.29537860068
1 0.773463595437 1.60575229327 1.39931286599
1 1.20908819348 1.22614197949 1.02950817453
1 1.16437641743 1.12178147108 1.09562891379
1 0.947235893443 1.26596960363 1.33223919372
1 0.828159800968 1.25201502894 1.3869174593
1 0.780803151339 0.587075533967 0.881474714822
1 0.68113961006 0.5006251904 0.86950588972
1 1.3673395559 0.378040991098 1.51693726094
1 1.33352156179 0.485049588735 1.59441102799
1 1.47586949531 0.39175532275 1.222188928
1 1.58466718004 0.431308601022 1.15432369766
1 0.712842297668 1.19142317977 0.671666130725
1 0.583473242392 1.21072326778 0.685453745388
1 1.42818645703 0.985092492299 1.14459347392
1 1.40604855634 1.03039180178 1.0221847815
1 0.501959939749 0.818277595369 0.98203043022
1 0.496883864198 0.884192532918 0.874850979928
1 1.3629141421 0.660376992858 0.741408540094
1 1.43287403107 0.754663287412 0.80945367769
1 0.88731882341 1.01235055682 0.761407270758
1 0.921746352774 0.989740039942 0.636936922452
1 0.902074180009 1.16786878448 0.686409132451
1 0.880754916562 1.28857258911 0.734293148969
1 1.20818239515 0.594553701384 0.661167196967
1 1.23049461801 0.478967860407 0.725150289409
1 0.800044934502 1.07074408489 0.951595386386
1 0.830195731645 0.943031936499 0.928683021359
1 0.646418525539 1.23949438107 1.36054429137
1 0.683390312426 1.34626527435 1.43572419863
1 1.24986798903 1.18033011204 1.80907744643
1 1.22760806282 1.2866260197 1.87128905324
1 0.625272230308 1.50671580408 1.54202382967
1 0.535658193142 1.43206825644 1.53148512338
1 1.4713100396 0.673917594692 0.538588328877
1 1.57402514978 0.751981264597 0.544835494026
1 0.949492265511 0.674646109061 2.01927876316
1 1.0533313306 0.647151440273 2.08902565752
1 0.863003249501 0.521055664624 1.28386834445
1 0.915682564398 0.527658159293 1.16331449074
1 1.53407033815 1.26134955827 0.900975781065
1 1.42385751278 1.25535329858 0.838775090546
1 1.83110787665 1.110282385 1.26734920286
1 1.82474283248 1.00062798294 1.19666672308
1 1.82245294994 0.769117895948 0.891854923332
1 1.76170404157 0.803360186846 1.00857690485
1 1.40859916055 0.85375351183 1.29727025014
1 1.33183749111 0.802479098264 1.21061545882
1 0.446815997021 1.21367328978 1.18704210811
1 0.358139576211 1.2353378973 1.2831327218
1 1.66086932607 0.922097112683 1.3729647463
1 1.67285642961 1.01279677081 1.29008411468
1 0.957590545984 0.632685153844 1.5060956064
1 0.933899400873 0.523855397218 1.57795696104
1 0.551201722912 1.10626459737 0.546421995058
1 0.537420031818 1.03579316589 0.432327962631
1 1.25434925363 1.20460235927 1.50925904614
1 1.3737658667 1.17283730495 1.48596918052
1 1.0930285516 0.750098754358 1.77176970856
1 1.07449065769 0.765123464103 1.64081863724
1 0.546249449954 1.66335714044 1.3301193176
1 0.539837355719 1.59276799919 1.21536616119
1 0.251858392851 0.879943302982 1.52049774904
1 0.232733811732 0.878230376062 1.3938625055
1 1.00160816437 1.20912948922 1.04366550452
1 0.879809684189 1.16527443049 1.06027476898
1 0.603268794638 0.750526859154 1.13895787496
1 0.585660731815 0.876426733913 1.13619165285
1 1.37529253969 0.488983600176 1.02619588397
1 1.39717259588 0.536500440037 0.915897251464
1 1.1347961446 1.04030303287 0.712572436787
1 1.2586348712 1.00216734929 0.714364908777
1 0.737165741462 1.46138696138 1.0475441729
1 0.76957561859 1.40887164472 1.16059464171
1 1.1214859696 0.641684916901 0.389652286498
1 1.11558770267 0.759554293741 0.441533019666
1 1.20594083201 0.843863859459 0.920729868328
1 1.12773880445 0.920750008462 0.980929577226
1 1.54368022882 1.42857944352 1.82970407542
1 1.52811452798 1.5493060962 1.77275572894
1 0.933341569915 0.323901262566 0.902686761669
1 0.880308702569 0.433772467251 0.848669820262
1 1.42239016011 0.958958890431 1.59115518058
1 1.39053955252 0.845954625461 1.64973030836
1 0.904962681515 0.791378668382 1.15554928409
1 0.984347053448 0.791743729479 1.2649901838
1 0.65924550655 1.26477194259 1.06843330061
1 0.567882070203 1.15486240395 1.0701736452
1 0.863088210405 0.879352892394 1.41566301662
1 0.793631994043 0.772252987171 1.38942947568
1 1.1214436584 0.328405375216 1.20715423281
1 1.01978683614 0.413442016721 1.25119926886
1 1.0790327658 1.41247715195 0.840384608875
1 1.19636343635 1.47734378702 0.889675049927
1 0.928021527942 0.707212114545 0.729177300883
1 0.798175963849 0.728686406255 0.710141488678
1 0.727429678773 0.844713976238 1.57712486884
1 0.662433148292 0.878843634702 1.6949460109
1 1.09760188539 0.914122804048 1.18704253123
1 1.22259553871 0.945083776191 1.17783011204
1 0.663454963951 0.989731239211 0.839021511018
1 0.599193209897 1.02499153776 0.734202010629
1 1.22917552381 0.615682902887 1.20064211488
1 1.25094929425 0.630362776292 1.07951680601
BASISSET
POB-TZVP
EXCHPERM
DFT
BLYP
CHUNKS
200
END
SHRINK
1 1
FMIXING
30
LEVSHIFT
6 1
END
END

INPUT for lc-blyp calculation

Water cube
CRYSTAL
0 0 0
1
11.8172 11.8172 11.8172 90. 90. 90.
165
8 0.966182090512 1.00021468707 1.4854507836
8 1.03919930271 1.40081195207 1.57239938395
8 1.2300162475 0.527247909826 1.33289637139
8 0.768640540906 1.65014267339 1.3298380327
8 1.15689283417 1.2052291575 1.08481399993
8 0.903492451681 1.21632146363 1.38370900044
8 0.762101766916 0.505654892868 0.887620671563
8 1.38305427682 0.459265985174 1.53107572014
8 1.50650348644 0.456861016146 1.17375080391
8 0.63803650611 1.15520588634 0.658485597265
8 1.45252310192 1.04503698 1.09088574282
8 0.446270182446 0.842531479538 0.927859729885
8 1.43138112243 0.708681921267 0.740832092205
8 0.937938767221 1.03809015672 0.702070372
8 0.863986223471 1.24494550316 0.67097527333
8 1.26616296585 0.550525843685 0.700526097553
8 0.808251954778 1.01392546458 0.888978438209
8 0.700633060285 1.30514241952 1.36784449785
8 1.27978945943 1.22268439224 1.87452839928
8 0.61985597265 1.42719138205 1.54634253461
8 1.52579096571 0.709874674204 0.49502242494
8 0.984720576786 0.61250702366 2.05818366449
8 0.900647784585 0.474448261856 1.22569508852
8 1.49653835088 1.28823308398 0.830222810818
8 1.79160029449 1.07211158312 1.2086718512
8 1.83282960431 0.803301205023 0.9671824967
8 1.34537504654 0.873155146735 1.24777189182
8 0.4377635142 1.24948481874 1.26121712419
8 1.61083522323 0.963454117727 1.32491478523
8 0.89343812409 0.582376366652 1.52855871103
8 0.492430694242 1.0714599059 0.497475290255
8 1.32287047693 1.24018718478 1.48182623633
8 1.08089682835 0.710079629692 1.69978937481
8 0.566233625563 1.66400610974 1.25198558034
8 0.188996462783 0.885536929222 1.46524041228
8 0.92452552212 1.23048649426 1.03169295603
8 0.617660274854 0.817834258538 1.08969459771
8 1.33952662221 0.537026114477 0.97252276343
8 1.21163067393 1.07015274346 0.705801289646
8 0.708953559219 1.40961251396 1.10277104559
8 1.06568992655 0.706494854957 0.400919507159
8 1.12978751312 0.876184290695 0.910686033917
8 1.55138340724 1.51283019666 1.84138306875
8 0.943388281488 0.379874928071 0.842503892631
8 1.35594709407 0.919504451139 1.62474444031
8 0.948775175168 0.840589733609 1.20458492706
8 0.622394898961 1.20107174288 1.02580848255
8 0.784972836205 0.848350032157 1.42938403344
8 1.08217014183 0.360261737129 1.27039222489
8 1.16518735403 1.41018464611 0.848232999357
8 0.851257319839 0.708795315303 0.771359374471
8 0.682134261923 0.819043512846 1.64355321057
8 1.15068908032 0.962640642453 1.15036303016
8 0.595814321497 0.971598517415 0.797778153877
8 1.22474054768 0.674640862472 1.14489794537
1 1.04184933825 0.980869495312 1.46944707714
1 0.966587770369 1.07866017331 1.46048801747
1 1.00937303253 1.3425173476 1.52038587821
1 0.996500440037 1.36528094642 1.63609315235
1 1.19357995126 0.452229885252 1.3260631114
1 1.2984623261 0.518463849304 1.38540804928
1 0.69602291575 1.63709626646 1.29537860068
1 0.773463595437 1.60575229327 1.39931286599
1 1.20908819348 1.22614197949 1.02950817453
1 1.16437641743 1.12178147108 1.09562891379
1 0.947235893443 1.26596960363 1.33223919372
1 0.828159800968 1.25201502894 1.3869174593
1 0.780803151339 0.587075533967 0.881474714822
1 0.68113961006 0.5006251904 0.86950588972
1 1.3673395559 0.378040991098 1.51693726094
1 1.33352156179 0.485049588735 1.59441102799
1 1.47586949531 0.39175532275 1.222188928
1 1.58466718004 0.431308601022 1.15432369766
1 0.712842297668 1.19142317977 0.671666130725
1 0.583473242392 1.21072326778 0.685453745388
1 1.42818645703 0.985092492299 1.14459347392
1 1.40604855634 1.03039180178 1.0221847815
1 0.501959939749 0.818277595369 0.98203043022
1 0.496883864198 0.884192532918 0.874850979928
1 1.3629141421 0.660376992858 0.741408540094
1 1.43287403107 0.754663287412 0.80945367769
1 0.88731882341 1.01235055682 0.761407270758
1 0.921746352774 0.989740039942 0.636936922452
1 0.902074180009 1.16786878448 0.686409132451
1 0.880754916562 1.28857258911 0.734293148969
1 1.20818239515 0.594553701384 0.661167196967
1 1.23049461801 0.478967860407 0.725150289409
1 0.800044934502 1.07074408489 0.951595386386
1 0.830195731645 0.943031936499 0.928683021359
1 0.646418525539 1.23949438107 1.36054429137
1 0.683390312426 1.34626527435 1.43572419863
1 1.24986798903 1.18033011204 1.80907744643
1 1.22760806282 1.2866260197 1.87128905324
1 0.625272230308 1.50671580408 1.54202382967
1 0.535658193142 1.43206825644 1.53148512338
1 1.4713100396 0.673917594692 0.538588328877
1 1.57402514978 0.751981264597 0.544835494026
1 0.949492265511 0.674646109061 2.01927876316
1 1.0533313306 0.647151440273 2.08902565752
1 0.863003249501 0.521055664624 1.28386834445
1 0.915682564398 0.527658159293 1.16331449074
1 1.53407033815 1.26134955827 0.900975781065
1 1.42385751278 1.25535329858 0.838775090546
1 1.83110787665 1.110282385 1.26734920286
1 1.82474283248 1.00062798294 1.19666672308
1 1.82245294994 0.769117895948 0.891854923332
1 1.76170404157 0.803360186846 1.00857690485
1 1.40859916055 0.85375351183 1.29727025014
1 1.33183749111 0.802479098264 1.21061545882
1 0.446815997021 1.21367328978 1.18704210811
1 0.358139576211 1.2353378973 1.2831327218
1 1.66086932607 0.922097112683 1.3729647463
1 1.67285642961 1.01279677081 1.29008411468
1 0.957590545984 0.632685153844 1.5060956064
1 0.933899400873 0.523855397218 1.57795696104
1 0.551201722912 1.10626459737 0.546421995058
1 0.537420031818 1.03579316589 0.432327962631
1 1.25434925363 1.20460235927 1.50925904614
1 1.3737658667 1.17283730495 1.48596918052
1 1.0930285516 0.750098754358 1.77176970856
1 1.07449065769 0.765123464103 1.64081863724
1 0.546249449954 1.66335714044 1.3301193176
1 0.539837355719 1.59276799919 1.21536616119
1 0.251858392851 0.879943302982 1.52049774904
1 0.232733811732 0.878230376062 1.3938625055
1 1.00160816437 1.20912948922 1.04366550452
1 0.879809684189 1.16527443049 1.06027476898
1 0.603268794638 0.750526859154 1.13895787496
1 0.585660731815 0.876426733913 1.13619165285
1 1.37529253969 0.488983600176 1.02619588397
1 1.39717259588 0.536500440037 0.915897251464
1 1.1347961446 1.04030303287 0.712572436787
1 1.2586348712 1.00216734929 0.714364908777
1 0.737165741462 1.46138696138 1.0475441729
1 0.76957561859 1.40887164472 1.16059464171
1 1.1214859696 0.641684916901 0.389652286498
1 1.11558770267 0.759554293741 0.441533019666
1 1.20594083201 0.843863859459 0.920729868328
1 1.12773880445 0.920750008462 0.980929577226
1 1.54368022882 1.42857944352 1.82970407542
1 1.52811452798 1.5493060962 1.77275572894
1 0.933341569915 0.323901262566 0.902686761669
1 0.880308702569 0.433772467251 0.848669820262
1 1.42239016011 0.958958890431 1.59115518058
1 1.39053955252 0.845954625461 1.64973030836
1 0.904962681515 0.791378668382 1.15554928409
1 0.984347053448 0.791743729479 1.2649901838
1 0.65924550655 1.26477194259 1.06843330061
1 0.567882070203 1.15486240395 1.0701736452
1 0.863088210405 0.879352892394 1.41566301662
1 0.793631994043 0.772252987171 1.38942947568
1 1.1214436584 0.328405375216 1.20715423281
1 1.01978683614 0.413442016721 1.25119926886
1 1.0790327658 1.41247715195 0.840384608875
1 1.19636343635 1.47734378702 0.889675049927
1 0.928021527942 0.707212114545 0.729177300883
1 0.798175963849 0.728686406255 0.710141488678
1 0.727429678773 0.844713976238 1.57712486884
1 0.662433148292 0.878843634702 1.6949460109
1 1.09760188539 0.914122804048 1.18704253123
1 1.22259553871 0.945083776191 1.17783011204
1 0.663454963951 0.989731239211 0.839021511018
1 0.599193209897 1.02499153776 0.734202010629
1 1.22917552381 0.615682902887 1.20064211488
1 1.25094929425 0.630362776292 1.07951680601
BASISSET
POB-TZVP
EXCHPERM
DFT
LC-wBLYP
CHUNKS
200
END
GUESSP
SHRINK
1 1
FMIXING
30
LEVSHIFT
6 1
END
END

And I also post the run.sh file for killdevil here.

#!/bin/bash -l
#BSUB -n "60"
#BSUB -e err.%J  
#BSUB -o out.%J
#BSUB -q week

CRYSTAL=/nas02/home/y/i/yiy/software/crystal/CRYSTAL14_amd64/bin/Linux-ifort_amd64/v1.0.3/Pcrystal
#/usr/mpi/intel/mvapich2-1.7/bin/mpiexec -n 10 $CRYSTAL > cubo.out1 &> cubo.out2
mpirun $CRYSTAL > H2O55.out1 &> H2O55.out2

A script to transfer xyz file to crystal structure file.

species_dict = {'O':8, 'H':1, 'Na':17, 'Cl':11}
#read box size
file_box = file("box")
line = file_box.readline()
words = line.split()
cell_a = float(words[0])
cell_b = float(words[1])
cell_c = float(words[2])
file_box.close()

#read coordinate
file_coordinate = file("NaCl_NVT_34000.xyz")
line = file_coordinate.readline()
words = line.split()
natoms = int(words[0])
file_coordinate.readline()
for i in range(natoms):
    line = file_coordinate.readline()
    words = line.split()
    species = words[0]
    x = float(words[1])
    y = float(words[2])
    z = float(words[3])
    print species_dict[species], x/cell_a, y/cell_b, z/cell_c

box file is like this.

12.4934 12.4934 12.4934