Linker IT Software
Google
Web www.oraxcel.com
menubar-top-links menubar-top-rechts
Home Help Search Login
Welcome, Guest. Please Login.
SQL*XL: Database to Excel bridge litLIB: Excel power functions pack ExcelLock: Locking and securing your valuable Excel spreadsheets encOffice: Protect your Excel file easy and safe encOffice: Protect your Excel file easy and safe
Pages: 1 2 
The crystal program (Read 35651 times)
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
The crystal program
22.04.10 at 08:17:55
 
The crystal program
 
Crystal is a computational chemistry package with which one can do periodic claculations in a crystal. It is possible to calculate various properties such as band structures, the density of states, phonon modes, crystal orbitals, etc.  
 
Reference to User's Manual:
Dovesi, R.; Saunders, V. R.; Roetti, C.; Orlando, R.; Zicovich-Wilson, C. M.; Pascale, F.; Civalleri, B.; Doll, K.; Harrison, N. M.; Bush, I. J.; D’Arco, P.; Llunell, M. CRYSTAL 2009 User’s Manual; University of Torino: Torino, 2009.
 
More crystal notes:
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1271917075/20
 
See also:
Crystal home page
http://www.crystal.unito.it/
Back to top
 
« Last Edit: 01.04.12 at 09:25:49 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
Crystal06 documentation
Reply #1 - 22.04.10 at 08:27:58
 
Crystal06 documentation
 
Tutorials on how to run the crystal program can be found here:
http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/index.html
 
A quick tutorial on how to perform a single point calculation can be found here:
http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/others/quick.htm l
 
The user's manual
http://www.crystal.unito.it/Manuals/crystal09.pdf
Back to top
 
« Last Edit: 22.04.10 at 08:38:38 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
Running crystal06
Reply #2 - 22.04.10 at 08:30:12
 
Running crystal06
 
Input is taken from a text input file called project.d12
 
To run the program run: runcry06 project
 
The output can be found in project.out
The wavefunction is saved (in binary form) in project.f9
 
To track the state of the running program you can grep the output file for CYC:
grep CYC *.project.out
 
Usage
 
runcry09 inpfilename  [wf_filename]
 
This script controls a CRYSTAL run
 
The program crystal is executed for wave function and total energy calculation (and geometry optimization, if required). If execution is successful, and an input file with the same name of the crystal input file (inpfilename.d12), but extension d3 (inpfilename.d3), is present, the program properties is executed.
 
inpfilename.d12      crystal HF/KS wave function calculation input deck
[wf_filename.f9] (optional)      wave function data from a previous run - see "SCF", keyword GUESSP, RESTART  
[inpfilename.d3] (optional)      properties  input deck
inpfilename.out      printed output file
 
The following files (if they exist) are saved in the current directory at the end of the calculation (fort.9 is binary, all other files are formatted):
 
file      program      saved as      data stored      keyword
fort.9      crystal      inpfilename.f9      binary wave function      default, if SCF successful
fort.98      crystal      inpfilename.f98      formatted w-f      default, if SCF successful
GAUSS98.DAT      crystal      inpfilename.gjf      input for  Gaussian98        GAUSS98
fort.33      crystal      inpfilename.xyz      atoms coordinates        COORPRT
FINDSYM.DAT      crystal      inpfilename.FINDSYM      input for findsym      FINDSYM
fort.34      crystal      inpfilename.gui      GUI - crystal structure      EXTPRT
HESSOPT.DAT      crystal      inpfilename.hessopt      Hessian      OPTGEOM
OPTINFO.DAT      crystal      inpfilename.optinfo      info for opt restart      OPTGEOM
FREQINFO.DAT      crystal      inpfilename.freqinfo      info for frequencies restart      FREQCALC
HESSFREQ.DAT      crystal      inpfilename.hessfreq      Hessian      FREQCALC
REFLECTANCE.DAT      crystal      inpfilename.reflectance      reflectance data to plot      FREQCALC/REFLECTANCE
EOSINFO.DAT      crystal      inpfilename.eosinfo      Equation of State      EOS
ELASINFO.DAT      crystal      inpfilename.elasinfo      elastic constants      ELASTCON
 
See also:
How to run crystal
http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/others/howtorun. html
Back to top
 
« Last Edit: 10.10.10 at 12:49:34 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
Crystal06 single point calculations
Reply #3 - 22.04.10 at 08:32:26
 
Crystal06 single point calculations
 
Input to the crystal06 program is a text file called project.d12.
 
The input contains a title line (free format) and then 3 input blocks:
  • Geometry input
    • Dimensionality of the system
      CRYSTAL : denotes a 3D calculation
    • Crystallographic information (3D only)
      0 0 0 : spacegroup id is sequential = 0, type of cell for rhombohedral cells = 0, origin of the crystal reference frame is derived from the space group = 0
    • Space Group number
      See appendix A of the user manual
    • Lattice parameter(s) (Angstrom and degrees)
      a,b,c    : translation vectors separated by a comma
      alpha, beta  : crystallographic angles alpha and beta, separated by a comma
      gamma    : crystallographic angle gamma
    • Number of non equivalent atoms
    • Conventional atomic number and fractional coordinates of the atoms  

  • Basisset input
    See: Crystal tutorial project
    http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/basis_set/basis_ set_tut.html
     
    Minimum basissets:
    http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1271917075/0#4
  • Single particle Hamiltonian and SCF control

 
 
Source:
A quick tour of CRYSTAL: Wave function calculation input and output
http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/others/quick.htm l
User's manual
http://www.crystal.unito.it/Manuals/crystal09.pdf
Back to top
 
« Last Edit: 22.04.10 at 16:08:37 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
CRYSTAL: Minimum basissets
Reply #4 - 22.04.10 at 16:07:48
 
CRYSTAL: Minimum basissets
 
Minimum basissets to be used in CRYSTAL calculations.
 
  • Z=1 (H)
    1 1
    1 0 3  1.  0.
  • Z=2 (He)
    2 1
    1 0 3  2.  0.
  • Z=3 (Li)
    3 2
    1 0 3  2.  0.
    1 1 3  1.  0.
  • Z=4 (Be)
    4 2
    1 0 3  2.  0.
    1 1 3  2.  0.
  • Z=5 (B)
    5 2
    1 0 3  2.  0.
    1 1 3  3.  0.
  • Z=6 (C)
    6 2
    1 0 3  2.  0.
    1 1 3  4.  0.
  • Z=7 (N)
    7 2
    1 0 3  2.  0.
    1 1 3  5.  0.
  • Z=8 (O)
    8 2
    1 0 3  2.  0.
    1 1 3  6.  0.
  • Z=9 (F)
    9 2
    1 0 3  2.  0.
    1 1 3  7.  0.
  • Z=10 (Ne)
    10 2
    1 0 3  2.  0.
    1 1 3  8.  0.
  • Z=11
    11 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  1.  0.
  • Z=12
    12 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
  • Z=13
    13 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  3.  0.
  • Z=14
    14 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  4.  0.
  • Z=15
    15 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
  • Z=16
    16 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
  • Z=17
    17 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  7.  0.
  • Z=18
    18 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
  • Z=19
    19 4
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  1.  0.
  • Z=20
    20 4
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
  • Z=21
    21 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  1.  0.
  • Z=22
    22 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  2.  0.
  • Z=23
    23 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  3.  0.
  • Z=24
    24 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  4.  0.
  • Z=25
    25 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  5.  0.
  • Z=26
    26 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  6.  0.
  • Z=27
    27 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  7.  0.
  • Z=28 (Ni)
    28 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  8.  0.
  • Z=29
    29 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  9.  0.
  • Z=30
    30 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  2.  0.
    1 3 3  10.  0.
  • Z=31
    31 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  3.  0.
    1 3 3  10.  0.
  • Z=32
    32 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  4.  0.
    1 3 3  10. 0.
  • Z=33
    33 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
    1 3 3  10. 0.
  • Z=34
    34 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
    1 3 3  10. 0.
  • Z=35
    35 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  7.  0.
    1 3 3  10. 0.
  • Z=36
    36 5
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 3 3  10. 0.
  • Z=37
    37 6
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  1. 0.
    1 3 3  10.  0.
  • Z=38
    38 6
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
  • Z=39
    39 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  1.  0.
  • Z=40
    40 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  2.  0.
  • Z=41
    41 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  3.  0.
  • Z=42
    42 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  4.  0.
  • Z=43
    43 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  5.  0.
  • Z=44
    44 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  6.  0.
  • Z=45
    45 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  7.  0.
  • Z=46
    46 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  8.  0.
  • Z=47
    47 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  9.  0.
  • Z=48
    48 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  2. 0.
    1 3 3  10.  0.
    1 3 3  10. 0.
  • Z=49
    49 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  3. 0.
    1 3 3  10.  0.
    1 3 3  10. 0.
  • Z=50
    50 7
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  8.  0.
    1 1 3  8  0.
    1 1 3  4. 0.
    1 3 3  10.  0.
    1 3 3  10. 0.
     
    See also:
    6-21G basisset
    http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1271917075/15#16
  • Back to top
     
    « Last Edit: 31.12.11 at 21:11:33 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Geometry optimisations with CRYSTAL
    Reply #5 - 05.10.10 at 12:51:36
     
    Geometry optimisations with CRYSTAL
     
    Geometry optimisations can be done in several ways with CRYSTAL. With the least input you just need to add the following to the input just after the basisset details:
     
    OPTGEOM
    END
     
    You can specify the following options in this input block:
    FULLOPTG        full geometry optimization –
    CELLONLY        cell parameters optimization –
    INTREDUN        optimization in redundant internal coordinates 115      –
    ITATOCEL          iterative optimization (atom/cell) –
    CVOLOPT          full geometry optimization at constant volume
    TOLDEE      threshold on energy change between optimisation steps (default 7 -> E-07)
    TOLDEG     convergence criterion on the RMS of the gradient (default 0.0003)
    TOLDEX     convergence criterion on the RMS of the displacement (default 0.0012)
    NOTRUSTR    do not use a trust radius
     
    Full input:
    Code:
    PROJECT=rta-pf6a ; export PROJECT
    
    cd /scratch
    
    rm $PBS_O_WORKDIR/$PROJECT.out
    
    cat<<EOF>$PROJECT.d12
    RT (edottf)2pf6  3-21G  HF
    CRYSTAL
    0 0 0
    2
    7.197, 7.343, 11.948
    93.454, 75.158
    97.405
    24
    15     0	  0	 0
    9     0.011     -0.206  -0.0141
    9     -0.033    -0.024  0.1296
    9     0.2161    0.0342  -0.0041
    16	0.78266 0.3429  0.5233
    16	0.61043 0.18828 0.31157
    16	0.38869 0.31205 0.67984
    16	0.21736 0.15751 0.46308
    8	 0.9282  0.4323  0.7036
    8	 0.5442  0.4084  0.8564
    6	 0.5348  0.2855  0.541
    6	 0.463   0.2191  0.4495
    6	 0.7619  0.3859  0.6697
    6	 0.422   0.1053  0.2504
    6	 0.583   0.3753  0.7403
    6	 0.2425  0.0914  0.3195
    6	 0.8996  0.432   0.8245
    6	 0.7274  0.499   0.8899
    1	 0.114401645     0.042498368     0.291452192
    1	 0.45618995	0.069093225     0.159758289
    1	 0.700178069     0.472070635     0.980725446
    1	 1.022960428     0.516115619     0.84400179
    1	 0.726667076     0.644021933     0.878942923
    1	 0.904844258     0.292116632     0.847550344
    OPTGEOM
    END
    END
    1 1
    1 0 3  1.  0.
    6 2
    1 0 3  2.  0.
    1 1 3  4.  0.
    8 2
    1 0 3  2.  0.
    1 1 3  6.  0.
    9 2
    1 0 3  2.  0.
    1 1 3  7.  0.
    15 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
    16 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
    99 0
    END
    SHRINK
    8 8
    END
    EOF
    
    runcry09 $PROJECT
    
    cp $PROJECT.out $PBS_O_WORKDIR
    cp $PROJECT.f9  $PBS_O_WORKDIR
    
     
    
    

     
    To track the progress of the geometry optimisation, first grep the output file for CYC to see whether the initial SCF converges. If it does, then grep for TOTAL to see the total energy convergence:
     
    grep CYC project.out
    grep TOTAL project.out
     
    You can also VIEW the progress of the optimisation by loading in the (partial) output file into J-Ice.
     
    Rerun to get the final energy after an optimisation!
    The energy calculated at the end of a geometry optimisation may be wrong.  
     
    Crystal Manual:
    "A safe procedure to check if that geometry corresponds to a real energy minimum, is to perform a second optimization process, with same truncation criteria, starting from the geometry obtained in the first optimization (read from file fort.34, keyword EXTERNAL, page 15)."
     
    When the energy changes a lot (in the order 1E-03 / 1E-04) during the optimisation it is best to only allow a few steps (10 or 15). Then stop and restart the optimisation at the last geometry. When it is close to convergence (in the order of 1E-05/1E-06) longer runs are possible.
    You can restrict the number of iterations by adding MAXCYCLE followed on the next line by the number of iterations you would like to allow. Add this after the OPTGEOM keyword.
     
    Always perform a final single point calculation, with the final optimized geometry, allows to check the calculated total energy. The FINALRUN keyword allows you to achieve this automatically. The following input will do a geometry optimisation and after the optimisation it is restarted automatically to check that it is all correct:
     
    OPTGEOM
    FINALRUN
    4
    END
     
    It appears that even after a complete run with the FINALRUN 4 option the energy can be lowered slightly by performing another geometry optimisation run. It will take one step as essentially it is converged but the energy is lower still. Example: After a 80 step geometry optimisation with FINALRUN 4 option the energy is A. Restarting using the external coordinates in the .gui file and with the vectors in the .f9 file results in convergence in 1 step with energy B that is 0.5E-06 lower:
    A:-9,942.444145145
    B:-9,942.444146572
    Back to top
     
    « Last Edit: 13.09.11 at 16:04:18 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Crystal: SCF convergence criterium
    Reply #6 - 05.10.10 at 15:58:06
     
    Crystal: SCF convergence criterium
     
    The SCF convergence criterium can be entered by giving the ITOLDEE keyword followed by a number on the next line. If e.g. 6 is given the convergence criterium is E-06.
     
    Full input file:
    Code:
    
    PROJECT=rtb-pf6a ; export PROJECT
    
    cd /scratch
    
    rm $PBS_O_WORKDIR/$PROJECT.out
    
    cat<<EOF>$PROJECT.d12
    RT (edottf)2pf6  3-21G  HF
    CRYSTAL
    0 0 0
    2
    7.197, 7.343, 11.948
    93.454, 75.158
    97.405
    24
    15	   0		 0			  0
    9	    0.01	   -0.20		    -0.01
    9	   -0.03	   -0.02		     0.12
    9	    0.21	    0.03		    -0.00
    16	   0.78	    0.34		     0.52
    16	   0.61	    0.18		     0.31
    16	   0.38	    0.31		     0.64
    16	   0.21	    0.15		     0.46
    8	    0.92	    0.43		     0.70
    8	    0.54	    0.40		     0.85
    6	    0.53	    0.28		     0.54
    6	    0.46	    0.21		     0.44
    6	    0.76	    0.38		     0.66
    6	    0.42	    0.10		     0.25
    6	    0.58	    0.37		     0.74
    6	    0.24	    0.09		     0.31
    6	    0.88	    0.50		     0.82
    6	    0.71	    0.39		     0.89
    1	    0.11	    0.04		     0.29
    1	    0.45	    0.06		     0.15
    1	    0.70	    0.47		     0.98
    1	    1.02	    0.51		     0.84
    1	    0.72	    0.64		     0.87	  
    1	    0.90	    0.29		     0.84	  
    END
    1 1
    1 0 3  1.  0.
    6 2
    1 0 3  2.  0.
    1 1 3  4.  0.
    8 2
    1 0 3  2.  0.
    1 1 3  6.  0.
    9 2
    1 0 3  2.  0.
    1 1 3  7.  0.
    15 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
    16 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
    99 0
    END
    SHRINK
    8 8
    TOLDEE
    5
    END
    EOF
    
    runcry09 $PROJECT
    
    cp $PROJECT.out $PBS_O_WORKDIR
    cp $PROJECT.f9  $PBS_O_WORKDIR
    
     
    
    
    Back to top
     
    « Last Edit: 05.10.10 at 16:20:11 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Crystal: Density matrix convergence criterium
    Reply #7 - 05.10.10 at 21:30:15
     
    Crystal: Density matrix convergence criterium
     
    The TOLDEP parameter can be used to set the convergence criterium of the density matrix.
    Add the TOLDEP keyword and on th enext line the value, e.g. 5 to set the threshold to 1E-05.
     
    The default value is 16 (i.e. 1E-16).
    Back to top
     
    « Last Edit: 20.11.10 at 15:09:31 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Running Crystal Parallel
    Reply #8 - 06.10.10 at 15:16:45
     
    Running Crystal Parallel
     
    To run Crystal parallel the runmpi script should be used and not the runcry.
    For version 9 these scripts are called runmpi09 en runcry09.
     
    runmpi09 takes as parameters the number of nodes and the input file.
    As an example the following command runs the job myjob on 10 nodes.
     
    runmpi09 10 myjob
     
    When running a geometry optimisation in parallel this way the convergence can be monitored from opta* files that are created. Run the following command to track the convergence:
     
    head -n 1 opta*
     
    The optaXXXX files can also be used to restart from. They are geometry files. See the section on geometry files for further details.
     
    If an error occurs in a parallel calculation you can find the error information in the file ERROR. You will need to copy that file manually from the scratch directory.
    Back to top
     
    « Last Edit: 10.10.10 at 20:35:05 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Direct SCF with Crystal
    Reply #9 - 06.10.10 at 17:10:39
     
    Direct SCF with Crystal
     
    To run crystal using direct SCF the SCFDIR keyword needs to be added to the input.
     
    Example input
    Code:
    PROJECT=ltfb-ltb-ltpf6b ; export PROJECT
    
    cd /scratch
    
    rm $PBS_O_WORKDIR/$PROJECT.out
    
    cat<<EOF>$PROJECT.d12
    LT (edottf)2pf6  3-21G  HF
    CRYSTAL
    0 0 0
    2
    9.822, 11.000, 11.487
    101.865, 99.128
    90.445
    47
       1     -2.912623731946E-01  2.082936754322E-01  1.861711239261E-01
       1	2.644065905003E-01  1.825363549241E-03 -1.024246357474E-01
       1	2.014381475920E-01  1.404166274085E-01 -2.069445588826E-02
       1	4.651851259193E-01  5.729538838184E-02  1.019010805477E-01
       1	8.913795417161E-03  7.123890153942E-03 -1.638274726309E-01
       1	2.772395878005E-02  1.545168461598E-01 -2.023139139910E-01
      16	2.269399276834E-01  1.406603631469E-02  4.967985947922E-01
      16	3.594212023755E-01  3.257481398339E-02  2.743499087061E-01
      16	4.409271864502E-01  1.909935248694E-01 -3.377176065404E-01
      16     -4.160663977805E-01  2.111110258079E-01  4.188473257558E-01
       6	3.802868818763E-01  1.063104985739E-01 -4.820368287512E-01
       6	4.355943487074E-01  1.214339705172E-01  4.175371153450E-01
       6	2.073407580386E-01  5.779352701689E-02 -3.492351470674E-01
       6	4.826156656788E-01  8.880042198234E-02  1.998419262969E-01
       6	3.073573235035E-01  1.313133095436E-01 -2.743189936665E-01
       6     -4.097679171005E-01  1.741901116464E-01  2.612202083200E-01
       6	7.761729367787E-02  6.616387545526E-02 -1.969503851591E-01
       6	2.173980056567E-01  9.069693790570E-02 -1.096964010998E-01
       8	9.611398826950E-02  5.233621052241E-04 -3.168077595483E-01
       8	3.118609637795E-01  1.700142386527E-01 -1.483129365231E-01
      15     -2.675227911853E-01  2.359195247545E-01  8.712916583113E-03
       9     -3.851813478132E-01  1.237481761880E-01 -1.403324607808E-02
       9     -1.429028269581E-01  3.487076978818E-01  4.715281094551E-02
       9     -2.875906189524E-01  2.477735828361E-01 -1.301223801409E-01
       9     -2.790814601290E-01  2.095174944238E-01  1.742993416685E-01
       9     -1.504334789198E-01  1.332849783720E-01 -1.061657274017E-02
       9     -3.756043136602E-01  3.367358735886E-01  4.303711909922E-02
       1	4.840682203209E-01  4.018466399947E-01  1.265812682476E-01
       1	4.272841335387E-01 -4.456336163662E-01  1.075233537758E-01
       1	2.736302996966E-01  3.762362534033E-01 -2.097984595567E-02
       1	1.845862406221E-01  4.883548959410E-01  7.039309533477E-02
       1     -1.306852980090E-01  3.095930291443E-01 -2.471814296362E-01
       1	4.897607474631E-02  4.740979348840E-01 -1.337034474693E-01
      16	3.105418056092E-01  4.752856815700E-01  4.681393029794E-01
      16	1.696619286312E-01  4.755492223102E-01 -3.037328298711E-01
      16	1.073549537573E-01  2.777113684420E-01  3.153299188300E-01
      16     -3.972702416846E-02  2.801016055452E-01 -4.427400147595E-01
       6	4.013552494734E-01  4.702542181231E-01  1.446387340456E-01
       6	2.599288552799E-01  4.151942364438E-01  7.080125389369E-02
       6	2.211248869706E-01  3.478372276992E-01  2.435735466515E-01
       6     -4.957628570969E-02  3.469064761420E-01 -2.896230414363E-01
       6	1.651610976413E-01  3.730259952907E-01  4.595020836810E-01
       6	1.066266185091E-01  3.738517874747E-01 -4.433276214058E-01
       6	3.106389767531E-01  4.425376674380E-01  3.125926822535E-01
       6	4.471318534467E-02  4.277266917126E-01 -2.279043221015E-01
       8	4.025907172580E-01 -4.873377043593E-01  2.715739882092E-01
       8	2.078052343841E-01  3.138365228237E-01  1.193912704320E-01
    OPTGEOM
    FULLOPTG
    END
    END
    1 1
    1 0 3  1.  0.
    6 2
    1 0 3  2.  0.
    1 1 3  4.  0.
    8 2
    1 0 3  2.  0.
    1 1 3  6.  0.
    9 2
    1 0 3  2.  0.
    1 1 3  7.  0.
    15 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
    16 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
    99 0
    END
    SHRINK
    8 8
    TOLDEP
    4
    SCFDIR
    END
    EOF
    
    #runcry09 $PROJECT
    runmpi09 10 $PROJECT
    
    
    cp $PROJECT.out $PBS_O_WORKDIR
    cp $PROJECT.f9  $PBS_O_WORKDIR
     
    
    
    Back to top
     
    « Last Edit: 06.10.10 at 17:11:45 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Crystal: change the max SCF iterations
    Reply #10 - 07.10.10 at 21:17:25
     
    Crystal: change the max SCF iterations
     
    The maximum number of SCF iterations can be changed using the MAXCYCLE keyword followed on the next line with the new maximum number. The default is 50.
     
    Full input file:
    Code:
    PROJECT=ltfa-ltb-ltpf6a ; export PROJECT
    
    cd /scratch
    
    rm $PBS_O_WORKDIR/$PROJECT.out
    
    #Density matrix from previous run (copy fort.9 to fort.20)
    #cp $PBS_O_WORKDIR/noconv3.f9 fort.20
    
    cat<<EOF>$PROJECT.d12
    LT (edottf)2pf6  3-21G  HF
    CRYSTAL
    0 0 0
    2
    9.822, 11.000, 11.487
    101.865, 99.128
    90.445
    47
    1	 0.148107147     -0.060484203    0.821013259
    1	 -0.019100619    -0.001934953    0.807876749
    1	 0.152191606     0.137006624     0.959960613
    1	 0.073112582     0.207376248     0.843428431
    1	 0.708602149     0.24728117	0.298619955
    1	 0.535471458     0.100426647     0.142699521
    16	0.22011	   0.030229961     0.493089946
    16	0.395549959     0.060249979     0.287319988
    16	0.42199998	0.19655	   0.673240002
    16	0.593899932     0.227329992     0.465280024
    6	 0.370099941     0.122400029     0.525000011
    6	 0.444199992     0.134799991     0.435300011
    6	 0.19309993	0.058099995     0.640999995
    6	 0.53039999	0.124999996     0.237200036
    6	 0.284399991     0.135600035     0.723099986
    6	 0.620999983     0.201499984     0.318600018
    6	 0.086099946     0.014299979     0.796899959
    6	 0.139199977     0.13380005	0.864299939
    8	 0.08069992	0.003200023     0.665499955
    8	 0.2779	    0.167700037     0.842300012
    15	0.76003 0.22885 -0.02141
    9	 0.645   0.1232  -0.0342
    9	 0.8754  0.3321  -0.012
    9	 0.7593  0.1935  -0.1659
    9	 0.7565  0.2546  0.114
    9	 0.8854  0.1386  -0.0062
    9	 0.634   0.3123  -0.0455
    1	 0.498117635     0.361588613     0.151169515
    1	 0.483723306     0.513007325     0.123120816
    1	 0.306873062     0.365336545     -0.00996298
    1	 0.232961455     0.486028536     0.083168085
    1	 -0.159929462    0.328697833     0.720330518
    1	 0.024967079     0.481003672     0.847957345
    16	0.32745997	0.457910057     0.473109973
    16	0.171969907     0.463250005     0.694569947
    16	0.115439981     0.276860012     0.313199947
    16	-0.044470012    0.284920038     0.544969975
    6	 0.433499938     0.441400006     0.155099954
    6	 0.296899983     0.405900007     0.082199993
    6	 0.23579995	0.345900056     0.246899982
    6	 -0.067800001    0.354400058     0.690500011
    6	 0.174399996     0.367400067     0.457300028
    6	 0.109500005     0.370299994     0.552600011
    6	 0.328599975     0.428399992     0.317900009
    6	 0.028499946     0.433900062     0.756999979
    8	 0.427200008     0.491899993     0.280399969
    8	 0.224999964     0.313600033     0.124500005
    OPTGEOM
    FULLOPTG
    END
    END
    1 1
    1 0 3  1.  0.
    6 2
    1 0 3  2.  0.
    1 1 3  4.  0.
    8 2
    1 0 3  2.  0.
    1 1 3  6.  0.
    9 2
    1 0 3  2.  0.
    1 1 3  7.  0.
    15 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
    16 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
    99 0
    END
    SHRINK
    8 8
    MAXCYCLE
    100
    END
    EOF
    
    runmpi09 50 $PROJECT
    #runcry09 $PROJECT
    
    cp $PROJECT.out $PBS_O_WORKDIR
    cp $PROJECT.f9  $PBS_O_WORKDIR
    
     
    
    
    Back to top
     
     

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Crystal: SCF FAILED - OPTGEOM STOP
    Reply #11 - 08.10.10 at 08:34:29
     
    Crystal: SCF FAILED - OPTGEOM STOP
     
    When a geometry optimisation in Crystal is performed, the following message can be received:
     
     ERROR **** OPTGEOM **** SCF FAILED - OPTGEOM STOP
     
    To my experience this is due to the last geometry in the optimisation to have gone astray. Copying the one but last geometry back into the input file and running the geometry optimisation again will skip passed this error. Is this an error in the optimisation routine?
    Back to top
     
     

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Crystal: warning FLAT SURFACE
    Reply #12 - 08.10.10 at 09:04:47
     
    Crystal: warning FLAT SURFACE
     
    At the end of a geometry optimisation check the output for the following warning. The optimisation completes successfully however you may not be at a minimum! Usually when I copy the 'converged' coordinates back into the input and rerun the optimisation I reach lower energies.
     

     MAX GRADIENT      0.002957  THRESHOLD              0.000450 CONVERGED NO
     RMS GRADIENT      0.000499  THRESHOLD              0.000300 CONVERGED NO
     MAX DISPLAC.      0.002956  THRESHOLD              0.001800 CONVERGED NO
     RMS DISPLAC.      0.000499  THRESHOLD              0.001200 CONVERGED YES
     
    WARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNING
     
     FLAT SURFACE - NO CHANGE IN ENERGY FOR   4 STEPS
     CONVERGENCE TESTS NOT SATISFIED AFTER  70 ENERGY AND GRADIENT CALCULATIONS
     
     WARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNINGWARNING
    Back to top
     
    « Last Edit: 08.10.10 at 09:05:19 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Crystal: restart using input vectors
    Reply #13 - 08.10.10 at 15:30:37
     
    Crystal: restart using input vectors
     
    Crystal can be (re)started using input vectors from a previous run. To do this you must supply the .f9 file with input vectors. An .f9 is usually created after a successful calculation. In the input file, specify the GUESSP keyword so the program reads from the supplied .f9 file.
     
    Full input
    Code:
    PROJECT=ltfa-ltb-ltpf6a ; export PROJECT
    
    #cd /scratch
    cd $TMPDIR
    
    rm $PBS_O_WORKDIR/$PROJECT.out
    
    #Density matrix from previous run (the run script will copy this to fort.9 or fort.20)
    cp $PBS_O_WORKDIR/$PROJECT.f9 . 
    
    cat<<EOF>$PROJECT.d12
    LT (edottf)2pf6  3-21G  HF
    CRYSTAL
    0 0 0
    2
    10.06559882 12.40681417 12.18069322
    93.635691 88.468747
    95.122555
    47
       1	2.293886802426E-01  4.489661246441E-02 -4.933634329138E-02
       1	7.172709526373E-02  9.896711252814E-02 -4.269025068066E-02
       1	2.777972059703E-01  2.382897888519E-01 -5.151186663298E-05
       1	1.892036273927E-01  2.574137697641E-01 -1.161067480820E-01
       1     -3.916862738544E-01  1.456339282151E-01  1.732908232276E-01
       1	3.880112412497E-01  1.426366782899E-03  1.354243684186E-01
      16	2.386521391873E-01  1.409964035404E-02 -4.091931817995E-01
      16	3.267544666114E-01 -3.714390528922E-03  3.327293789752E-01
      16	4.784878341871E-01  1.781517250179E-01 -3.618980703026E-01
      16     -4.343563400475E-01  1.584460445616E-01  3.747258802651E-01
       6	3.869072274840E-01  8.876274433068E-02 -4.588986114244E-01
       6	4.245586703154E-01  8.061415973582E-02  4.293014366579E-01
       6	2.496323123888E-01  7.781580476426E-02 -2.732813402391E-01
       6	4.254847367630E-01  3.820962050383E-02  2.170641754967E-01
       6	3.576482035190E-01  1.520444621937E-01 -2.520261335430E-01
       6     -4.660170467387E-01  1.107875805872E-01  2.360116131026E-01
       6	1.716917829531E-01  9.491752919705E-02 -8.756644891693E-02
       6	2.525605332123E-01  2.071612774308E-01 -8.504416782932E-02
       8	1.408521491423E-01  4.885888002701E-02 -1.997511850816E-01
       8	3.814589555772E-01  2.111609880130E-01 -1.498022128609E-01
      15     -2.207332233290E-01  1.724657902483E-01 -2.859549572215E-02
       9     -3.111856605238E-01  5.413788237579E-02 -2.705729441405E-02
       9     -1.326364796489E-01  2.887353204465E-01 -2.910552908987E-02
       9     -1.691896766837E-01  1.387697511775E-01 -1.569482004245E-01
       9     -2.766221812354E-01  2.016961286739E-01  1.002381428969E-01
       9     -9.046246690805E-02  1.301480774982E-01  1.661935859845E-02
       9     -3.547358772279E-01  2.109243283076E-01 -7.229289222911E-02
       1	4.760847351833E-01 -4.423321172223E-01  1.284866263254E-01
       1	3.785259719944E-01 -3.442845863805E-01  1.029653178368E-01
       1	2.917843197293E-01  4.776359831011E-01  1.360480540461E-03
       1	1.653718274997E-01 -4.746278488176E-01  9.578284548052E-02
       1     -6.055649659023E-02  2.211221838525E-01 -2.413363828348E-01
       1	3.251532281702E-02  3.976256525133E-01 -1.484349125503E-01
      16	2.768639523504E-01 -4.606332574173E-01  4.543764023686E-01
      16	1.506206284008E-01  4.651679238735E-01 -3.144394167206E-01
      16	1.774309130349E-01  3.267939769324E-01  3.359419943594E-01
      16	4.337387055739E-02  2.535785633297E-01 -4.273889247532E-01
       6	3.757107289839E-01 -4.161227637332E-01  1.413537489616E-01
       6	2.642658558111E-01  4.969851481786E-01  8.901348325332E-02
       6	2.481763173987E-01  4.281622630024E-01  2.557087298012E-01
       6	3.252763436471E-03  2.811157189838E-01 -2.845257745172E-01
       6	1.889240177166E-01  4.103302915289E-01  4.637279418851E-01
       6	1.358503842429E-01  3.803348286385E-01 -4.408778929670E-01
       6	2.923487953632E-01 -4.787505808453E-01  3.079455062799E-01
       6	5.130263565442E-02  3.738442570385E-01 -2.356116560973E-01
       8	3.467301814467E-01 -3.893684270686E-01  2.581636530444E-01
       8	2.530522215265E-01  4.023824273032E-01  1.401413560513E-01
    END
    1 1
    1 0 3  1.  0.
    6 2
    1 0 3  2.  0.
    1 1 3  4.  0.
    8 2
    1 0 3  2.  0.
    1 1 3  6.  0.
    9 2
    1 0 3  2.  0.
    1 1 3  7.  0.
    15 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
    16 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
    99 0
    END
    SHRINK
    8 8
    MAXCYCLE
    100
    GUESSP
    END
    EOF
    
    runmpi09 50 $PROJECT $PROJECT
     
    
    

     
    Note that runmpi09 is called with 3 parameters. The number of cores (50) the input file ($PROJECT) and the name of the file with input vectors ($PROJECT): name.f9.
     
    The error " ERROR **** GUESSP **** COPY OF WAVEFUNCTION FILE fort.20 CAN NOT BE FOUND" means that you have either not copied the $PROJECT.f9 file to the scratch directory or that you have omitted the input vectors parameter to the run script.
     
    Vectors from a smaller or larger basisset can also be read in and used as a starting density using the GUESDUAL command. Example:
    GUESDUAL
    1 1
    6 2 2
    The first line indicates that for 1 atom the basis set is different. The second one indicates a normal SCF run should be performed. 0 should be used for cryscor (see manual).
    The next line, 6 means atom number 6 (C), 2 means that changes apply from shell 2 and the last 2 means that there are 2 additional shells that are not in the input vector file .f9.
    Back to top
     
    « Last Edit: 15.03.12 at 18:17:17 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Gerrit-Jan Linker
    YaBB Administrator
    *****




    Posts: 75
    Crystal: using external geometry file
    Reply #14 - 10.10.10 at 15:35:35
     
    Crystal: using external geometry file
     
    Geometry information can be read from a file and as such be used as input. This can be handy in case you wish to restart after a geometry optimisation for example. Recalculation is ALWAYS necessary after a geometry optimisation.
     
    The geometry files are created by crystal itself. The program will create a fortran file that is renamed by the run script to .gui. Simply copy this file back into the scratch directory to use it as input. The EXTERNAL keyword is used to denote that the geometry input should be read in. Also the optaXXXX files created when using OPTGEOM can be used as input. Rename these files to $PROJECT.gui to restart from them.
     
    Full input file used to read in a .gui file  
    Code:
    PROJECT=rtb-pf6b ; export PROJECT
    
    cd $TMPDIR
    
    rm $PBS_O_WORKDIR/$PROJECT.out
    
    cp $PBS_O_WORKDIR/$PROJECT.f9 .
    cp $PBS_O_WORKDIR/$PROJECT.gui .
    
    cat<<EOF>$PROJECT.d12
    RT (edottf)2pf6  3-21G  HF
    EXTERNAL
    END
    1 1
    1 0 3  1.  0.
    6 2
    1 0 3  2.  0.
    1 1 3  4.  0.
    8 2
    1 0 3  2.  0.
    1 1 3  6.  0.
    9 2
    1 0 3  2.  0.
    1 1 3  7.  0.
    15 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  5.  0.
    16 3
    1 0 3  2.  0.
    1 1 3  8.  0.
    1 1 3  6.  0.
    99 0
    END
    SHRINK
    8 8
    END
    EOF
    
    runcry09 $PROJECT
    #runcry09 $PROJECT $PROJECT
    #runmpi09 50 $PROJECT
    #runmpi09 50 $PROJECT $PROJECT
    
    cp * $PBS_O_WORKDIR
     
    
    

     
    The last line ensures all files that exist in the scratch directory will be copied back. This will include the .gui file or the optaXXXX files.
    Back to top
     
    « Last Edit: 10.10.10 at 19:55:44 by Gerrit-Jan Linker »  

    Gerrit-Jan Linker
    Linker IT Software
    Email WWW Gerrit-Jan Linker   IP Logged
    Pages: 1 2