Crystal17
Software computing electronic wave function and properties of periodic systems
Introduction
CRYSTAL is a program designed for use in modeling crystalline solids. The program will compute the electronic structure of periodic structures using one of a number of different approximations including Hartree-Fock, Density Functional Theory or one of a number of hybrid approximations such as global, range-separated or double-hybrids. The program is also quite versatile and capable of modeling the physical and chemical properties not just of crystalline solids but also of nanotubes, surfaces, molecules and polymers. See the Main Website for additional details.
License
Crystal is a licensed software. The license file is installed on all nodes of the partition mendoza_q. Currently only members of Professor Jose Mendoza Cortes' research group have access to this software.
Currently, there are two major releases of Crystal available at the RCC, Crystal14, and Crystal17.
Usage of Crystal14 at the RCC
The installed package contains 5 utilities: the serial version crystal, properties, parallel version Pcrystal, Pproperties, and the massively parallel version MPPcrystal.
There is one version currently available, 1_0_4d. To use these utilities, first include the bin directory to you PATH variable:
If you use version 1_0_4d
$ export PATH=/gpfs/research/mendozagroup/crystal/2014/v1_0_4d/bin/Linux-ifort_XE_emt64/v1.0.4/:$PATH
Next check if they are available by a command like the following:
$ which Pcrystal
If not found, then something is wrong. If it is working, then it is better to include this line to your .bashrc file for future use.
To submit a crystal job, You need first provide an input data file. For Pcrystal and MPPcrystal, the input file has be to called INPUT. Since there will be many temporary data/filescreated when the programming is running, it is better to create a scratch directory, run the code in the scratch directory, and copy the useful output to user's home directory upon a successful run.
Note. To run the parallel version of Crystal14, you need to load the intel-openmpi module.
If you use version 1_0_4d
$ module load intel/15
$ module load intel-openmpi
Here is a sample input data file test00.d12:
TEST00 - CO MOLECULE - NO BIPOLAR EXPANSION
MOLECULE
1
2
6 0. 0. 0.
8 0.8 0.5 0.4
END
6 4
0 0 3 2. 1.
72. 0.15
13 0.53
3.5 0.44
0 1 2 4. 1.
1.1 0.049 0.51
0.29 0.96 0.61
0 2 1 0. 1.
0.4 1.
0 3 1 0. 1.
0.6 1.
8 4
0 0 3 2. 1.
131. .15
24. .53
6.4 .44
0 1 2 6. 1.
1.9 0.049 0.51
0.49 0.96 0.61
0 2 1 0. 1.
0.7 1.
0 3 1 0. 1.
0.8 1.
99 0
END
NOBIPOLA
TOLINTEG
20 20 20 20 20
TOLDEE
7
FMIXING
10
NODIRECT
END
Here is an example SLURM submit script slurm.sub asking for 4 compute nodes and 64 cores in total:
#!/bin/bash
#SBATCH -J crys14
#SBATCH -o crys14-%J.o
#SBATCH -N 4
#SBATCH --ntasks-per-node=16
#SBATCH -p mendoza_q
#SBATCH -t 4:00:00
#SBATCH --mail-type=ALL
export JOB=test00
export DIR=$SLURM_SUBMIT_DIR
export scratch=/gpfs/research/mendozagroup/scratch/crystal/$USER/v1_0_4
echo "submit directory: "
echo $SLURM_SUBMIT_DIR
module purge
module load intel/15
module load intel-openmpi
# remove the following line if already in your .bashrc file
#export PATH=/gpfs/research/mendozagroup/crystal/v1_0_3/crystal14-1.0.3/bin/Linux-ifort_emt64/v1.0.3:$PATH
export PATH=/gpfs/research/mendozagroup/crystal/v1_0_4/bin/Linux-ifort_XE_emt64/v1.0.4:$PATH
mkdir -p $scratch/$JOB
# the following line need be modified according to where your input is located
cp $DIR/../test_cases/inputs/${JOB}.d12 $scratch/$JOB/INPUT
cd $scratch/$JOB
touch hostfile
rm hostfile
for i in `scontrol show hostnames $SLURM_JOB_NODELIST`
do
echo "$i slots=16" >> hostfile
done
# in the following, -np parameters should be equal to those specified above.
mpirun -np 64 -machinefile hostfile Pcrystal 2>&1 > $DIR/${JOB}.out
cp fort.9 ${DIR}/${JOB}.f9
# uncomment the next 5 lines if you want to remove the scratch directory
#if [ $? -eq 0 ]
#then
# cd ${DIR}
# rm -rf $scratch/${JOB}
#fi
Upon a successful run, you will see things similar to the following in the SLURM output file crys14-$JOBID.o:
64 PROCESSORS WORKING
*******************************************************************************
* *
* CRYSTAL14 *
* public : 1.0.4 - Feb 23rd, 2016 *
* HTTP://WWW.CRYSTAL.UNITO.IT *
* *
* MAIN AUTHORS *
....
.... skipped many things here
.... near the end
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TOTENY TELAPSE 10.39 TCPU 5.66
CYC 9 ETOT(AU) -1.107649354541E+02 DETOT -4.46E-09 tst 5.98E-10 PX 2.50E-04
== SCF ENDED - CONVERGENCE ON ENERGY E(AU) -1.1076493545406E+02 CYCLES 9
TOTAL ENERGY(HF)(AU)( 9) -1.1076493545406E+02 DE-4.5E-09 tst 6.0E-10 PX 2.5E-04
EIGENVECTORS IN FORTRAN UNIT 10
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT END TELAPSE 11.51 TCPU 5.69
EEEEEEEEEE TERMINATION DATE 12 05 2016 TIME 16:36:53.0
NODE 0 CPU TIME = 5.693
TOTAL CPU TIME = 336.350
Example Input Data
Crystal developers have provided some test input data, to copy them to your own directory, use things like
cd $HOME
mkdir -p crystal14
cp -r /gpfs/research/mendozagroup/crystal/v1_0_4/test_cases ~/crystal14/
Usage of Crystal17 at the RCC
The usage of Crystal17 is essentially the same as Crystal14, you only need to set environment as the following
If you use version 1.0.1
export PATH=/gpfs/research/mendozagroup/crystal/2017/v1_0_1_amended/ifort14/bin/Linux-ifort14_XE_emt64/v1.0.1:$PATH
module purge
module load intel/16
modula load intel-openmpi
If you use version 1.0.2
export PATH=/gpfs/research/mendozagroup/crystal/2017/v1_0_2/ifort14/bin/Linux-ifort14_XE_emt64/v1.0.2:$PATH
module purge
module load intel/16
modula load intel-openmpi
An example of Crystal17
The submit script BG_test.sh
#!/bin/bash
#SBATCH -J BG_Test
#SBATCH -o BG_Test-%J.o
#SBATCH -N 1
#SBATCH -n 4
#SBATCH -p backfill
#SBATCH -t 04:00:00
cat $SLURM_JOB_NODELIST
export JOB=BG_Test
export DIR=$SLURM_SUBMIT_DIR
export PATH=/gpfs/research/mendozagroup/crystal/2017/v1_0_1_amended/ifort14/bin/Linux-ifort14_XE_emt64/v1.0.1:$PATH
export scratch=/gpfs/research/mendozagroup/scratch/crystal/${USER}/crys17
echo "submit directory: "
echo $SLURM_SUBMIT_DIR
module purge
module load intel/16
module load intel-openmpi
rm -fr $scratch/$JOB
mkdir -p $scratch/$JOB
# the following line need be modified according to where your input is located
cp $DIR/${JOB}.d12 $scratch/$JOB/INPUT
#cp $DIR/${JOB}.f9 $scratch/$JOB/fort.9
cd $scratch/$JOB
which Pcrystal
srun Pcrystal >& $DIR/${JOB}.out
cp fort.9 ${DIR}/${JOB}.f9
The input data file BG_test.d12
Crystal17 Test Cakculations BLG-1V
CRYSTAL
0 0 0
191
4.99095 3.45003
3
6 0.16872 0.33745 0.00000
6 0.33333 0.66667 0.00000
23 0.00000 0.00000 0.50000
END
23 14
0 0 8 2.0 1.0
232340.65058 0.00023072410092
34828.841170 0.00178881789620
7926.5448691 0.00929924901310
2243.7733046 0.03776146334700
730.59322944 0.12255909662000
262.32219631 0.28963508811000
101.70403805 0.41004702955000
40.064784617 0.21113610858000
0 0 4 2.0 1.0
255.24014968 -0.02445811633800
78.804646961 -0.11527205366000
12.340598946 0.55174749453000
5.1742019219 0.54504528489000
0 0 2 2.0 1.0
7.6513894469 -0.22967638286000
1.2639759898 0.71683769077000
0 0 1 2.0 1.0
2.0363959000 1.00000000000000
0 0 1 0.0 1.0
0.5857304500 1.00000000000000
0 0 1 0.0 1.0
0.2750729900 1.00000000000000
0 2 6 6.0 1.0
1184.2369151 0.00244498267290
280.23075192 0.01964345446600
89.643627137 0.09079694919000
33.242411253 0.25650768222000
13.144514452 0.40815393750000
5.2948534140 0.23860378268000
0 2 3 6.0 1.0
20.175586851 -0.02824148902300
2.7605865197 0.55574635619000
1.1008900902 0.99319919270000
0 2 1 0.0 1.0
0.7153797600 1.00000000000000
0 2 1 0.0 1.0
0.2384599200 1.00000000000000
0 3 4 3.0 1.0
43.861134864 0.01148717423800
12.516021891 0.06824715397700
4.3313854957 0.21837784195000
1.6138855773 0.39245212296000
0 3 1 0.0 1.0
0.5790593700 1.00000000000000
0 3 1 0.0 1.0
0.2143837300 1.00000000000000
0 4 1 0.0 1.0
0.8310000000 1.00000000000000
28 14
0 0 8 2.0 1.0
351535.72935 0.00022529386884
52695.809283 0.00174686162230
11992.468293 0.00908499921360
3394.5776689 0.03694074844700
1105.3594585 0.12032819950000
397.14677769 0.28596715057000
154.27542974 0.40983020196000
61.018723780 0.21620642851000
0 0 4 2.0 1.0
384.45559739 -0.02465127926800
119.04879199 -0.11658505277000
19.137012223 0.54864126676000
8.1526718562 0.52640051122000
0 0 2 2.0 1.0
12.579408642 -0.22797884293000
2.0870866081 0.70703738215000
0 0 1 2.0 1.0
2.9480296700 1.00000000000000
0 0 1 0.0 1.0
0.87308901 1.00000000000000
0 0 1 0.0 1.0
0.16787354 1.00000000000000
0 2 6 6.0 1.0
1883.0907486 0.00237482584430
445.95155320 0.01928945717200
143.08430815 0.09071821150700
53.372920722 0.26181414117000
21.321919357 0.42309149832000
8.6643561994 0.24641686015000
0 2 3 6.0 1.0
34.144255211 -0.02967712916300
4.7122455921 0.55616824096000
1.8709231845 0.96357766460000
0 2 1 0.0 1
1.0453650800 1.00000000000000
0 2 1 0.0 1.0
0.4276468400 1.00000000000000
0 3 4 8.0 1
74.591603465 0.01207745467200
21.590632752 0.07463726215400
7.6246142580 0.23236775502000
2.8632206762 0.39042651680000
0 3 1 0.0 1
1.0075942000 1.00000000000000
0 3 1 0.0 1
0.3167209900 1.00000000000000
0 4 1 0.0 1.0
2.1740000000 1.00000000000000
24 14
0 0 8 2.0 1.0
254477.80704 0.00023386945693
38131.797054 0.00181426018000
8675.2930607 0.00943639257210
2455.0099848 0.03834363936700
799.16217787 0.12459194837000
286.90021489 0.29489696029000
111.25413232 0.41846149607000
43.864152636 0.21633763420000
0 0 4 2.0 1.0
279.32669173 -0.02345090811100
86.274732376 -0.11080370027000
13.555756113 0.53028965842000
5.6978112751 0.51603516947000
0 0 2 2.0 1.0
8.5636582615 -0.38109545675000
1.3988296768 1.19915914360000
0 0 1 2.0 1.0
1.5142137900 1.00000000000000
0 0 1 0.0 1.0
0.5047379300 1.00000000000000
0 0 1 0.0 1.0
0.1505787700 1.00000000000000
0 2 6 6.0 1.0
1306.4398864 0.00242773261850
309.25311441 0.01954404101700
98.996273963 0.09065179455300
36.756916451 0.25699279154000
14.566657077 0.40935504891000
5.8739937432 0.23729388849000
0 2 3 6.0 1.0
22.890999695 -0.02816602661300
3.0855001822 0.56034120148000
1.2132329118 0.98119019650000
0 2 1 0.0 1.0
0.4593168100 1.00000000000000
0 2 1 0.0 1.0
0.2296584050 1.0000000000000
0 3 4 4.0 1.0
43.720074476 0.01362296402600
12.391242652 0.07893518013300
4.2639442006 0.23833840000000
1.5525221790 0.39526851122000
0 3 1 0.0 1.0
1.1288617700 1.00000000000000
0 3 1 0.0 1.0
0.5172623600 1.00000000000000
0 4 1 0.0 1.0
1.1470000000 1.00000000000000
27 14
0 0 8 2.0 1.0
325817.01553 0.00022568462484
48839.636453 0.00174993975330
11114.937307 0.00910031340970
3146.1603642 0.03699625683700
1024.4378465 0.12044269621000
368.02508816 0.28598731649000
142.91229205 0.40908312004000
56.482649209 0.21500145739000
0 0 4 2.0 1.0
356.40298318 -0.02476705967800
110.31165215 -0.11702139134000
17.659634834 0.55215522200000
7.5059030479 0.53246877060000
0 0 2 2.0 1.0
11.501807176 -0.22942470077000
1.9081994606 0.71180933514000
0 0 1 2.0 1.0
2.6083233500 1.00000000000000
0 0 1 0.0 1.0
0.7955677300 1.00000000000000
0 0 1 0.0 1.0
0.1356673700 1.00000000000000
0 2 6 6.0 1.0
1731.1369144 0.00239057676850
409.91750438 0.01938299996700
131.45648578 0.09090544850900
48.987439714 0.26146681577000
19.537078992 0.42157264570000
7.9287281634 0.24571813557000
0 2 3 6.0 1.0
31.076017584 -0.02943806997300
4.2835180697 0.55615568168000
1.7022921563 0.96772195064000
0 2 1 0.0 1.0
1.1628100700 1.00000000000000
0 2 1 0.0 1.0
0.7018644100 1.00000000000000
0 3 4 7.0 1.0
68.140745239 0.01198384536000
19.685241019 0.07368854047500
6.9322128825 0.23085496779000
2.6025125694 0.39281059225000
0 3 1 0.0 1.0
0.9207081800 1.00000000000000
0 3 1 0.0 1.0
0.2922317400 1.00000000000000
0 4 1 0.0 1.0
1.9030000000 1.00000000000000
26 14
0 0 8 2.0 1.0
300784.84637 0.00022806273096
45088.970557 0.00176817887610
10262.516317 0.00919270834900
2905.2897293 0.03735549580700
946.11487137 0.12151108426000
339.87832894 0.28818881468000
131.94425588 0.41126612677000
52.111494077 0.21518583573000
0 0 4 2.0 1.0
329.48839267 -0.02474521647700
101.92332739 -0.11683089050000
16.240462745 0.55293621136000
6.8840675801 0.53601640182000
0 0 2 2.0 1.0
10.470693782 -0.22912708577000
1.7360039648 0.71159319984000
0 0 1 2.0 1.0
1.7565166800 1.00000000000000
0 0 1 0.0 1.0
0.77548354 1.00000000000000
0 0 1 0.0 1.0
0.1058918100 1.00000000000000
0 2 6 6.0 1.0
1585.3959970 0.00237939601790
375.38006499 0.01925315475500
120.31816501 0.09002183653600
44.788749031 0.25798172356000
17.829278584 0.41492649744000
7.2247153786 0.24207474784000
0 2 3 6.0 1.0
28.143219756 -0.02904175515200
3.8743241412 0.55312260343000
1.5410752281 0.96771136842000
0 2 1 0.0 1.0
0.9336590800 1.00000000000000
0 2 1 0.0 1.0
0.1999999900 1.00000000000000
0 3 4 6.0 1.0
61.996675034 0.01197197225500
17.873732552 0.07321013541000
6.2744782934 0.23103094314000
2.3552337175 0.39910706494000
0 3 1 0.0 1.0
0.8417158200 1.00000000000000
0 3 1 0.0 1.0
0.2611100300 1.00000000000000
0 4 1 0.0 1.0
1.5980000000 1.00000000000000
6 8
0 0 6 2.0 1.0
13575.349682 0.00022245814352
2035.2333680 0.00172327382520
463.22562359 0.00892557153140
131.20019598 0.03572798450200
42.853015891 0.11076259931000
15.584185766 0.24295627626000
0 0 2 2.0 1.0
6.2067138508 0.41440263448000
2.5764896527 0.23744968655000
0 0 1 0.0 1.0
0.4941102000 1.00000000000000
0 0 1 0.0 1.0
0.1644071000 1.00000000000000
0 2 4 2.0 1.0
34.697232244 0.00533336578050
7.9582622826 0.03586410909200
2.3780826883 0.14215873329000
0.8143320818 0.34270471845000
0 2 1 0.0 1.0
0.5662417100 1.00000000000000
0 2 1 0.0 1.0
0.2673545000 1.00000000000000
0 3 1 0.0 1.0
0.8791584200 1.00000000000000
99 0
END
DFT
SPIN
B3LYP
LGRID
END
TOLINTEG
7 7 7 7 14
TOLDEE
7
SHRINK
0 30
15 15 15
SCFDIR
BIPOSIZE
110000000
EXCHSIZE
110000000
ATOMSPIN
1
9 1
SPINLOCK
3
4
MAXCYCLE
800
FMIXING
80
ANDERSON
PPAN
GRIMME
1.05 20. 25.
2
23 10.80 1.562
6 1.75 1.452
END
Upon a successful run, you will have an output file BG_test.out similar to the following
PROCESS 0 OF 4 WORKING
PROCESS 1 OF 4 WORKING
PROCESS 3 OF 4 WORKING
PROCESS 2 OF 4 WORKING
*******************************************************************************
* *
* CRYSTAL17 *
* public : 1.0.1 - Jun 21st, 2017 *
* HTTP://WWW.CRYSTAL.UNITO.IT *
* *
* MAIN AUTHORS *
* *
* *
* R. DOVESI(1,11), V.R. SAUNDERS(2), C. ROETTI(1,11), R. ORLANDO(1,11), *
* C.M. ZICOVICH-WILSON(1,3), F. PASCALE(4), B. CIVALLERI(1,11), *
* K. DOLL(5), N.M. HARRISON(2,6), I.J. BUSH(7), Ph. D'ARCO(8), *
* M. LLUNELL(9), M. CAUSA'(10), Y. NOEL(8), L. MASCHIO(1,11), A. ERBA(1,11) *
* M. RE'RAT(14), S. CASASSA(1,11) *
* *
..... skipped many lines
OVERLAP POPULATION CONDENSED TO ATOMS FOR FIRST 6 NEIGHBORS
ATOM A 1 C ATOM B CELL R(AB)/AU R(AB)/ANG OVPOP(AB)
7 C ( 0 1 0) 2.689 1.423 -0.022
5 C ( 0 0 0) 2.756 1.459 0.012
9 V ( 0 0 0) 4.269 2.259 0.003
3 C ( 1 1 0) 4.658 2.465 0.000
8 C ( 0 0 0) 4.716 2.496 -0.003
3 C ( 0 0 0) 4.774 2.526 0.004
ATOM A 7 C ATOM B CELL R(AB)/AU R(AB)/ANG OVPOP(AB)
1 C ( 0 -1 0) 2.689 1.423 -0.022
2 C ( 0 0 0) 4.716 2.496 -0.003
8 C ( 1 0 0) 5.445 2.882 0.002
9 V ( 0 0 0) 6.346 3.358 -0.002
7 C ( 0 0 -1) 6.520 3.450 0.004
1 C ( 0 -1 -1) 7.052 3.732 -0.001
ATOM A 9 V ATOM B CELL R(AB)/AU R(AB)/ANG OVPOP(AB)
1 C ( 0 0 0) 4.269 2.259 0.003
7 C ( 0 0 0) 6.346 3.358 -0.002
9 V ( 0 0 -1) 6.520 3.450 -0.003
1 C ( -1 -1 0) 7.884 4.172 -0.000
9 V ( -1 -1 0) 9.432 4.991 0.000
1 C ( 0 0 -1) 10.160 5.377 -0.000
EIGENVECTORS IN FORTRAN UNIT 10
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT END TELAPSE 771.47 TCPU 754.58
EEEEEEEEEE TERMINATION DATE 02 10 2017 TIME 13:47:10.6
NODE 0 CPU TIME = 754.578
NODE 1 CPU TIME = 756.583
NODE 2 CPU TIME = 756.196
NODE 3 CPU TIME = 756.438
TOTAL CPU TIME = 3023.795
Crgra2006
The package CrGraph processes data written by CRYSTAL09 in fortranunit 25, to give graphic outputs in postscript language. The paper sizeis A4 (210x297 mm), in portrait mode. The maximum size of the plot is 180x270mm.
Three scripts are supplied:
maps06 to draw contour maps
bands06 to plot band structures
doss06 to plot total and projected density of states
To use these utilities at RCC, you need to define some environmental variables first,
If you use bash,
# if you use version 1_0_3
$ cp /gpfs/research/mendozagroup/crystal/v1_0_3/crystal14-1.0.3/cry14.bashrc ~/.cry14.bashrc
# if you use version 1_0_4
$ cp /gpfs/research/mendozagroup/crystal/v1_0_4/cry14.bashrc ~/.cry14.bashrc
$ source ~/.cry14.bashrc
If you use Cshell,
# if you use version 1_0_3
$ cp /gpfs/research/mendozagroup/crystal/v1_0_3/crystal14-1.0.3/cry14.cshrc ~/.cry14.cshrc
# if you use version 1_0_4
$ cp /gpfs/research/mendozagroup/crystal/v1_0_4/cry14.cshrc ~/.cry14.cshrc
$ source ~/.cry14.cshrc
To test if your environment is properly set up,
$ which band06
You should see
/gpfs/research/mendozagroup/crystal/v1_0_3/crystal14-1.0.3/crgra2006/band06
or
/gpfs/research/mendozagroup/crystal/v1_0_4/crgra2006/band06