Difference between revisions of "CamCASP/PFIT"

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import>Am592
import>Am592
Line 12: Line 12:
 
==Assessing Models==
  
==Assessing Models==
 
===Local Models===
  
===Local Models===
  +
The PROCESS command file to produce the PFIT command file that follows:
  +
<pre>
  +
TITLE PROCESS file for H2
  +
! Usage: process < H2_daTZ.prss
  +
  +
  +
Set Global-data
  +
CamCASP /home/am592/CamCASP/5.5-dev/
  +
Units BOHR DEGREE
  +
Overwrite
  +
Echo Off
  +
End
  +
  +
Molecule H2
  +
Units BOHR
  +
H1 1.00 0.00000000 0.00000000 0.00000000 Type H
  +
H2 1.00 0.00000000 0.00000000 1.44873600 Type H
  +
End
  +
  +
Read nonlocal pols for H2
  +
! Use ascii file OUT/H2_daTZ_0.0005_1000_f11_NL4.pol
  +
Use ascii file H2_daTZ_NL4_000.pol
  +
Maximum rank 4
  +
Limit rank to 1
  +
Limit rank to 1 for sites +++
  +
H1 H2
  +
Frequencies STATIC
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! Use this command to split the P-2-P pol file into 11 parts:
  +
! P2P-Pols <point-2-point pol file> SPLIT
  +
End
  +
  +
Write
  +
File-prefix H2_daTZ
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PFIT file for H2 with cutoff 0.000001 and penalties
  +
End
  +
  +
Finish
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</pre>
  +
  +
The '''penalties''' option is needed in the '''PFIT''' command line to get PROCESS to use only one molecule. This needs to be changed. The file shown next is an edited copy of the output. When using non-local polarizabilities PROCESS will create the file for '''two molecules''' (in this case, the first one is repeated). The second molecule has been edited out in the file below. PROCESS needs to be fixed to do this correctly.
  +
 
<pre>
  
<pre>
 
 

Revision as of 21:20, 22 September 2010

CamCASP => PFIT

PFIT : Purpose

  • Refining local polarizability models against point-to-point polarizabilities calculated with the FDDS (using CamCASP).
    • Local polarizabilty models only.
  • Assessing polarizability models against the point-to-point polarizabilities.
    • Local and non-local models.
  • Calculate molecular and distributed <math>C_6</math> coefficients.
    • Local and non-local models.
    • Now not so relevant (though may still be useful) as the CASIMIR program does this and more.

Assessing Models

Local Models

The PROCESS command file to produce the PFIT command file that follows: 

TITLE  PROCESS file for H2
! Usage: process < H2_daTZ.prss


Set Global-data
   CamCASP /home/am592/CamCASP/5.5-dev/
   Units  BOHR  DEGREE
   Overwrite
   Echo Off
End

Molecule H2
  Units BOHR
  H1          1.00    0.00000000    0.00000000    0.00000000   Type H
  H2          1.00    0.00000000    0.00000000    1.44873600   Type H
End

Read nonlocal pols for H2
   ! Use ascii file OUT/H2_daTZ_0.0005_1000_f11_NL4.pol
   Use ascii file H2_daTZ_NL4_000.pol
   Maximum rank  4
   Limit rank to 1
   Limit rank to 1 for sites +++
       H1 H2                                                                    
   Frequencies STATIC
   ! Use this command to split the P-2-P pol file into 11 parts:
   ! P2P-Pols <point-2-point pol file> SPLIT
End

Write
   File-prefix H2_daTZ
   PFIT file for H2 with cutoff 0.000001 and penalties
End

Finish

The penalties option is needed in the PFIT command line to get PROCESS to use only one molecule. This needs to be changed. The file shown next is an edited copy of the output. When using non-local polarizabilities PROCESS will create the file for two molecules (in this case, the first one is repeated). The second molecule has been edited out in the file below. PROCESS needs to be fixed to do this correctly. 

 
 Allocate
    points          2000
    batches 1    
    rank               1
    sites              4
    parameters           32
 End
 
 Data H2_daTZ_000.p2p      ! Point-to-point pols for this frequency only
 
 #include H2_daTZ.sites    ! Sites of this molecule
 #include H2_daTZ.axes     ! Axis file
 
 Polarizabilities
     H1  H1    00   00 =   H1_H1_00_00_A
     H1  H1    00   10 =   H1_H1_00_10_A
     H1  H1    10   10 =   H1_H1_10_10_A
     H1  H1   11c  11c = H1_H1_11c_11c_A
     H1  H1   11s  11s = H1_H1_11s_11s_A
 
     H1  H2    00   00 =   H1_H2_00_00_A
     H1  H2    00   10 =   H1_H2_00_10_A
     H1  H2    10   00 =   H1_H2_10_00_A
     H1  H2    10   10 =   H1_H2_10_10_A
     H1  H2   11c  11c = H1_H2_11c_11c_A
     H1  H2   11s  11s = H1_H2_11s_11s_A
 
 
     H2  H2    00   00 =   H2_H2_00_00_A
     H2  H2    00   10 =   H2_H2_00_10_A
     H2  H2    10   10 =   H2_H2_10_10_A
     H2  H2   11c  11c = H2_H2_11c_11c_A
     H2  H2   11s  11s = H2_H2_11s_11s_A
 
 End

 Frequencies            0  omega0 0.5
 
 Fix
       H1_H1_00_00_A +++
             0.00045175
       H1_H1_00_10_A +++
             0.00049875
       H1_H1_10_10_A +++
             2.02890222
     H1_H1_11c_11c_A +++
             1.55715064
     H1_H1_11s_11s_A +++
             1.55715064
       H1_H2_00_00_A +++
            -0.00045175
       H1_H2_00_10_A +++
             0.00050214
       H1_H2_10_00_A +++
            -0.00049877
       H1_H2_10_10_A +++
             1.42282188
     H1_H2_11c_11c_A +++
             0.95223742
     H1_H2_11s_11s_A +++
             0.95223742
       H2_H2_00_00_A +++
             0.00045175
       H2_H2_00_10_A +++
            -0.00050211
       H2_H2_10_10_A +++
             2.02889987
     H2_H2_11c_11c_A +++
             1.55715064
     H2_H2_11s_11s_A +++
             1.55715064
 End
  Start
 
 Print parameters total
 Print Total Origin 0.0 0.0 0.0
 
 
 Finish

The output looks like: 

$ ~/CamCASP/5.5-dev/bin/pfit < NL.data 
Batch  1:  2000 points

Sites
H1            0.000000    0.000000    0.000000
*** Warning: type H was not defined

H2            0.000000    0.000000    1.448736
1 passes

Polarizability parameters
                  Sites       Components  Coefficient
  1  H1_H1_00_00_A
                H1      H1      00   00      1.000
  2  H1_H1_00_10_A
                H1      H1      00   10      1.000
  3  H1_H1_10_10_A
                H1      H1      10   10      1.000
  4  H1_H1_11c_11c_A
                H1      H1      11c  11c     1.000
  5  H1_H1_11s_11s_A
                H1      H1      11s  11s     1.000
  6  H1_H2_00_00_A
...
...
 15  H2_H2_11c_11c_A
                H2      H2      11c  11c     1.000
 16  H2_H2_11s_11s_A
                H2      H2      11s  11s     1.000
Fix H1_H1_00_00_A =      0.00045
Fix H1_H1_00_10_A =      0.00050
Fix H1_H1_10_10_A =      2.02890
Fix H1_H1_11c_11c_A =      1.55715
Fix H1_H1_11s_11s_A =      1.55715
Fix H1_H2_00_00_A =     -0.00045
Fix H1_H2_00_10_A =      0.00050
Fix H1_H2_10_00_A =     -0.00050
Fix H1_H2_10_10_A =      1.42282
Fix H1_H2_11c_11c_A =      0.95224
Fix H1_H2_11s_11s_A =      0.95224
Fix H2_H2_00_00_A =      0.00045
Fix H2_H2_00_10_A =     -0.00050
Fix H2_H2_10_10_A =      2.02890
Fix H2_H2_11c_11c_A =      1.55715
Fix H2_H2_11s_11s_A =      1.55715


Static polarizabilities

Response values:
Maximum          0.0129773408
Minimum         -0.0092483859
Range            0.0222257267
Min. magnitude   0.0000000005
Residuals               per cent of range
Maximum      0.00091849       4.133
Minimum     -0.00169831      -7.641
R.m.s.       0.00007701       0.346

Parameter values
H1_H1_00_00_A            0.00045175
H1_H1_00_10_A            0.00049875
H1_H1_10_10_A            2.02890222
H1_H1_11c_11c_A          1.55715064
H1_H1_11s_11s_A          1.55715064
H1_H2_00_00_A           -0.00045175
H1_H2_00_10_A            0.00050214
H1_H2_10_00_A           -0.00049877
H1_H2_10_10_A            1.42282188
H1_H2_11c_11c_A          0.95223742
H1_H2_11s_11s_A          0.95223742
H2_H2_00_00_A            0.00045175
H2_H2_00_10_A           -0.00050211
H2_H2_10_10_A            2.02889987
H2_H2_11c_11c_A          1.55715064
H2_H2_11s_11s_A          1.55715064

Total static molecular polarizability
     00        z         x         y
   0.00000   0.00000   0.00000   0.00000
   0.00000   6.90149   0.00000   0.00000
   0.00000   0.00000   5.01878   0.00000
   0.00000   0.00000   0.00000   5.01878
Mean polarizability       =   5.64635
Polarizability anisotropy =   1.88272

Total static molecular polarizability
     00        z         x         y
   0.00000   0.00000   0.00000   0.00000
   0.00000   6.90149   0.00000   0.00000
   0.00000   0.00000   5.01878   0.00000
   0.00000   0.00000   0.00000   5.01878
Mean polarizability       =   5.64635
Polarizability anisotropy =   1.88272

Non-Local Models

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