add CPMD addons 4.3 to GitHub

Author: CPMD-Org

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Car-Parrinello Molecular Dynamics 
+Copyright (c) 2022 CPMD (Car-Parrinello Molecular Dynamics)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,2 +1,14 @@
-# tests
-Test suite for the CPMD distribution
+CPMD Tests
+==============
+
+This repository contains a series of input files that can be used for testing the CPMD installation.
+
+
+## Copyright Notice
+
+The CPMD program is © 1990-2022 by IBM Corp. and © 1994-2001 by Max Planck Institute, Stuttgart. 
+
+
+## License
+
+The CPMD is freely distributed under the MIT License.

external-potential/H_MT_PBE

@@ -0,0 +1,34 @@
+
+test to illustrate the use of an external potential file.
+
+first run the wavefunction optimization for the normal case
+(single water molecule in gasphase) and create a cubefile
+from the file DENSITY with cpmd2cube.
+
+then compile the file mkextpot.f and run the program to create
+the external potential. you'll need to specify the cell dimensions,
+the origin and the real space mesh.
+
+now run the wavefunction optimization for the external potential
+case and create another cube file from DENSITY file.
+
+create a difference cube file from the two density cubefiles,
+e.g. using the cubman utility from the gaussian software package.
+
+this cubefile now contains the response of the electron density
+to the external potential and can be visualize with standard
+tools. see e.g. http://www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html
+for some examples.
+
+the script runme.sh performs all the commands described above,
+h2o-dens-diff.vmd contains an example visualization of the 
+density difference and h2o-dens-diff.png a sample snapshot image 
+of that visualization.
+
+both runs together take less than 20 minutes on an 
+600MHz alpha workstation or and 1.3GHz amd athlon pc
+and need about 220MB RAM.
+
+01/2004  [email protected]
+tested with cpmd v3.8.4, cpmd2cube-0.1.2-cvs (+ bochum patches)
+and vmd v1.8.2

external-potential/O_MT_PBE

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+#!/usr/local/bin/vmd
+# VMD script written by save_state $Revision: 1.1 $
+# VMD version: 1.8.2
+set viewplist {}
+set fixedlist {}
+display projection   Orthographic
+display nearclip set 0.000000
+display farclip  set 10.000000
+display depthcue   off
+mol new {h2o-dens-diff.cube} type cube waitfor all
+mol addfile {h2o-dens-extpot.cube} type cube waitfor all
+mol addfile {h2o-dens-nopot.cube} type cube waitfor all
+mol delrep 0 top
+mol representation CPK 0.600000 0.200000 25.000000 20.000000
+mol color Name
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol representation Isosurface 0.002000 0.000000 0.000000 0.000000
+mol color ColorID 12
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 1 top 0
+mol colupdate 1 top 0
+mol scaleminmax top 1 0.000000 0.000000
+mol smoothrep top 1 0
+mol drawframes top 1 {now}
+mol representation Isosurface -0.002000 0.000000 0.000000 0.000000
+mol color ColorID 13
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 2 top 0
+mol colupdate 2 top 0
+mol scaleminmax top 2 0.000000 0.000000
+mol smoothrep top 2 0
+mol drawframes top 2 {now}
+mol representation Isosurface 0.100000 1.000000 0.000000 0.000000
+mol color ColorID 7
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 3 top 0
+mol colupdate 3 top 0
+mol scaleminmax top 3 0.000000 0.000000
+mol smoothrep top 3 0
+mol drawframes top 3 {now}
+mol showrep top 3 0
+mol representation Isosurface 0.100000 2.000000 0.000000 0.000000
+mol color ColorID 3
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 4 top 0
+mol colupdate 4 top 0
+mol scaleminmax top 4 0.000000 0.000000
+mol smoothrep top 4 0
+mol drawframes top 4 {now}
+mol showrep top 4 0
+mol rename top {h2o-dens-diff.cube}
+set viewpoints([molinfo top]) {{{1.000000 0.000000 0.000000 -4.227511} {0.000000 1.000000 0.000000 -4.167324} {0.000000 0.000000 1.000000 -3.968829} {0.000000 0.000000 0.000000 1.000000}} {{0.490640 0.868967 -0.064525 0.000000} {-0.377160 0.278545 0.883271 0.000000} {0.785507 -0.409043 0.464405 0.000000} {0.000000 0.000000 0.000000 1.000000}} {{1.053002 0.000000 0.000000 0.000000} {0.000000 1.053002 0.000000 0.000000} {0.000000 0.000000 1.053002 0.000000} {0.000000 0.000000 0.000000 1.000000}} {{1.000000 0.000000 0.000000 0.120000} {0.000000 1.000000 0.000000 -0.010000} {0.000000 0.000000 1.000000 0.000000} {0.000000 0.000000 0.000000 1.000000}}}
+lappend viewplist [molinfo top]
+set topmol [molinfo top]
+# done with molecule 0
+foreach v $viewplist {
+  molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($v)
+}
+foreach v $fixedlist {
+  molinfo $v set fixed 1
+}
+unset viewplist
+unset fixedlist
+mol top $topmol
+unset topmol
+proc vmdrestoremycolors {} {
+  color Display {Background} silver
+}
+vmdrestoremycolors

external-potential/README

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+&CPMD
+  OPTIMIZE WAVEFUNCTION
+  RESTART WAVEFUNCTION COORDINATES LATEST
+  EXTERNAL POTENTIAL
+  RHOOUT
+&END
+
+&DFT
+  FUNCTIONAL PBE
+&END
+
+&SYSTEM
+  SYMMETRY
+   0
+  CUTOFF
+  120.0
+  CELL
+   15.0 1.0 1.0 0.0 0.0 0.0
+  MESH
+  108 108 108
+&END
+
+&ATOMS
+*O_MT_PBE  KLEINMAN-BYLANDER
+ LMAX=P
+ 1
+ 5.570575       5.593517       5.669178 
+
+*H_MT_PBE  KLEINMAN-BYLANDER
+ LMAX=S
+ 2
+ 5.562867       7.428055       5.669178
+ 7.340606       5.111259       5.669178
+&END

external-potential/h2o-dens-diff.cube.gz

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+REMARK pdb file created from cpmd Wannier file: DENSITY
+HETATM    1   O  MOL     1       3.917   3.929   3.969  1.00  0.00
+HETATM    2   H  MOL     1       3.913   4.900   3.969  1.00  0.00
+HETATM    3   H  MOL     1       4.853   3.674   3.969  1.00  0.00
+TER       4      MOL    99
+END

external-potential/h2o-dens-diff.png

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+&CPMD
+  OPTIMIZE WAVEFUNCTION
+  RHOOUT
+&END
+
+&DFT
+  FUNCTIONAL PBE
+&END
+
+&SYSTEM
+  SYMMETRY
+   0
+  CUTOFF
+  120.0
+  CELL
+   15.0 1.0 1.0 0.0 0.0 0.0
+  MESH
+  108 108 108
+&END
+
+&ATOMS
+*O_MT_PBE  KLEINMAN-BYLANDER
+ LMAX=P
+ 1
+ 5.570575       5.593517       5.669178 
+
+*H_MT_PBE  KLEINMAN-BYLANDER
+ LMAX=S
+ 2
+ 5.562867       7.428055       5.669178
+ 7.340606       5.111259       5.669178
+&END

external-potential/h2o-dens-diff.vmd

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+REMARK pdb file created from cpmd Wannier file: DENSITY
+HETATM    1   O  MOL     1       3.917   3.929   3.969  1.00  0.00
+HETATM    2   H  MOL     1       3.913   4.900   3.969  1.00  0.00
+HETATM    3   H  MOL     1       4.853   3.674   3.969  1.00  0.00
+TER       4      MOL    99
+END

external-potential/h2o-dens-extpot.cube.gz

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+C     example program to create a grid file for use as
+c     an external potential input in cpmd calculations.
+C     this (simple) example assumes an orthorhombic cell 
+C     and produces a linear potential in z-direction.
+C
+C     feel free to adapt for your own purposes.
+C     you have to make sure, that the grid used here
+C     matches the real space grid of your cpmd run.
+C     
+C     all parameters are in a.u.
+C
+C     it is advisable to compile (and run) this program with 
+C     the same flags and on the same platform as your cpmd binary.
+C     otherwise the binary grid data may be incompatible.
+C     
+C     01/2004 <[email protected]>
+C     
+      program mkextpot
+      implicit none
+      integer nn(3)
+      real*8 phi,origin(3),cell(3),delta(3), x, y
+      integer i,j,k
+      external phi
+      
+      print*, 'give cell [a, b, c] (in bohr)'
+      read*,(cell(i),i=1,3)
+
+      print*, 'give origin [x0,y0,z0] (in bohr)'
+      read*,(origin(i),i=1,3)
+
+      print*, 'give mesh [na,nb,nc]'
+      read*,(nn(i),i=1,3)
+
+      do i=1,3
+        delta(i) = cell(i)/dble(nn(i))
+      end do
+
+      print*,' '
+      print*,'input parameters:'
+      print*,'cell  :   ', (cell(i),i=1,3)
+      print*,'origin:   ', (origin(i),i=1,3)
+      print*,'mesh:     ', (nn(i),i=1,3)
+      print*,'dx,dy,dz: ', (delta(i),i=1,3)
+      print*,' '
+      print*,'writing extpot.unfo.grid...'
+
+      open(99,file='extpot.unfo.grid',
+     $     form='unformatted',status='unknown')
+
+      do i=1,nn(1)
+        x=dble(i-1)*delta(1)+origin(1)
+        do j=1,nn(2)
+          y=dble(j-1)*delta(2)+origin(2)
+          write(99) (phi(x,y,dble(k-1)*delta(3)+origin(3)),k=1,nn(3))
+        enddo
+      enddo
+      close(99)
+
+      stop 'external potential grid written'
+      end
+
+
+c     potential function
+      real*8 function phi(x,y,z)
+      real*8 x,y,z
+
+      phi = 0.01*z
+
+      return
+      end

external-potential/h2o-dens-extpot.in

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+#!/bin/sh
+
+# tested with cpmd v3.8.4
+# tested with cpmd2cube v0.1.3(?)
+# tested with vmd v1.8.2
+
+./cpmd.x h2o-dens-nopot.in > h2o-dens-nopot.out
+./cpmd2cube.x -halfmesh -rho -o h2o-dens-nopot DENSITY
+
+./mkextpot <<EOF
+15.0 15.0 15.0
+0.0 0.0 -7.5
+108 108 108
+EOF
+
+./cpmd.x h2o-dens-extpot.in > h2o-dens-extpot.out
+./cpmd2cube.x -halfmesh -rho -o h2o-dens-extpot DENSITY
+
+cubman <<EOF
+sub
+h2o-dens-nopot.cube
+yes
+h2o-dens-extpot.cube
+yes
+h2o-dens-diff.cube
+yes
+EOF
+
+echo "now run 'vmd -e h2o-dens-diff.vmd' to view the result"