Commit dedc6cf2 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

remove obsolete reax tools and rename pair_meam.txt to pair_meamc.txt

parent 93efe3e4

doc/src/pair_meam.txt→doc/src/pair_meamc.txt

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File moved.

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tools/reax/bondConnectCheck.f90

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Original line number Diff line number Diff line 
!# DEC.9, 2010

!# HLL

!# NCSU

!#

!# This is a program to read the output from 'fix reax/bond', TPRD, Lammps

!# The output is saved into file "bonds.reax", where each image is divided

!# into three parts: 

!# 

!# (1) Head, 7 Lines;

!# (2) Body, No._of_atom Lines;

!# (3) Tail, 1 Line

!# 

!# The total number of images is related with the output frequence and number of iterations. 

!# In this case, it is "number of iteration+1".

!#

!# Each line in Body part is made up of the following parameters:

!# id, type, nb, id_1, id_2, ... id_nb, mol, bo_1, bo_2, ... bo_nb, abo, nlp, q

!# abo = atomic bond order

!# nlp = number of lone pairs

!# q = atomic charge

!#

!# PLEASE DOUBLE CHECK YOUR OWN LAMMPS INPUT SCRIPT & OUTPUT AND MAKE CORRESPONDING CHSNGES



program main

implicit none



integer I, J, K, L

integer image, natom

integer headline, tailline

integer id, atype, nb, bd1, bd2, bd3, bd4, mol

double precision bo1, bo2, bo3, bo4, abo, nlp, q



open (unit=10, file='bonds.reax')



open (unit=20, file='N129.txt', status='unknown')

open (unit=21, file='N133.txt', status='unknown')

open (unit=22, file='N137.txt', status='unknown')

open (unit=23, file='N141.txt', status='unknown')

open (unit=24, file='N145.txt', status='unknown')

open (unit=25, file='N149.txt', status='unknown')

open (unit=26, file='N153.txt', status='unknown')

open (unit=27, file='N157.txt', status='unknown')



open (unit=30, file='reactionRecord.txt', status='unknown')



!# Make changes accordingly.

image = 1

headline = 7

tailline = 1

natom = 384



do I = 1, image+1



! Skip the head part

  do J = 1, headline

  read(10,*)

  end do 

  

! Each image has 'natom' lines

    do K = 1, natom

    

! read in the first three number each line to determine:

! (1) what type of atom it is, atype

! the correspondence in Lammps: 1-C, 2-H, 3-O, 4-N, 5-S

! (2) how many bonds it has, nb

! this 'nb' determines the following bond_link information & bond_order paramaters of the same line



  read(10,*) id, atype, nb



! TEST  

! write(*,*) id, atype, nb

  

  if (atype .eq. 4) then 

  

  backspace 10

  

! Should have some easier way to replace this "IF", I am just toooo lazy.

! Thanks to the fact that the maximum number of bonds is 4. ^-^

!??? is it possible that nb = 0 ??? KEEP THAT IN MIND.



  if (nb.eq.0) then 

  

  	read(10,*) id, atype, nb, mol, abo, nlp, q



  	if (id .eq. 129) then 

  	write(20, 200) id, atype, nb, mol, abo, nlp, q

  	elseif (id .eq. 133) then 

  	write(21, 200) id, atype, nb, mol, abo, nlp, q

  	elseif (id .eq. 137) then 

  	write(22, 200) id, atype, nb, mol, abo, nlp, q

  	elseif (id .eq. 141) then 

  	write(23, 200) id, atype, nb, mol, abo, nlp, q

  	elseif (id .eq. 145) then 

  	write(24, 200) id, atype, nb, mol, abo, nlp, q

  	elseif (id .eq. 149) then 

  	write(25, 200) id, atype, nb, mol, abo, nlp, q

  	elseif (id .eq. 153) then 

  	write(26, 200) id, atype, nb, mol, abo, nlp, q

  	elseif (id .eq. 157) then 

  	write(27, 200) id, atype, nb, mol, abo, nlp, q

  	200 format(4I4, 3f14.3)

    endif 

    

! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.

    write (30, 300)  I, id, atype, nb, mol, abo, nlp, q

    300 format(5I4, 3f14.3)



    

  elseif (nb.eq.1) then

  

    read(10,*) id, atype, nb, bd1, mol, bo1, abo, nlp, q



   	if (id .eq. 129) then 

  	write(20, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	elseif (id .eq. 133) then 

  	write(21, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	elseif (id .eq. 137) then 

  	write(22, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	elseif (id .eq. 141) then 

  	write(23, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	elseif (id .eq. 145) then 

  	write(24, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	elseif (id .eq. 149) then 

  	write(25, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	elseif (id .eq. 153) then 

  	write(26, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	elseif (id .eq. 157) then 

  	write(27, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q

  	201 format(5I4, 4f14.3) 

  	endif 

  	

 ! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.

    write (30, 301)  I, id, atype, nb, bd1, mol, bo1, abo, nlp, q

    301 format(6I4, 4f14.3)

    

  elseif (nb.eq.2) then

  

    read(10,*) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  

   	if (id .eq. 129) then 

  	write(20, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	elseif (id .eq. 133) then 

  	write(21, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	elseif (id .eq. 137) then 

  	write(22, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	elseif (id .eq. 141) then 

  	write(23, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	elseif (id .eq. 145) then 

  	write(24, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	elseif (id .eq. 149) then 

  	write(25, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	elseif (id .eq. 153) then 

  	write(26, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	elseif (id .eq. 157) then 

  	write(27, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

  	202 format(6I4, 5f14.3) 

  	endif 

  	

! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.

    write (30, 302)  I, id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q

    302 format(7I4, 5f14.3)

  	

  elseif (nb.eq.3) then

  

    read(10,*) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q



  

   	if (id .eq. 129) then 

  	write(20, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q

  	elseif (id .eq. 133) then 

  	write(21, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q

  	elseif (id .eq. 137) then 

  	write(22, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q

  	elseif (id .eq. 141) then 

  	write(23, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q

  	elseif (id .eq. 145) then 

  	write(24, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q

  	elseif (id .eq. 149) then 

  	write(25, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q

  	elseif (id .eq. 153) then 

  	write(26, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bd3, abo, nlp, q

  	elseif (id .eq. 157) then 

  	write(27, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q

  	203 format(7I4, 6f14.3) 

    endif 

  

 elseif (nb.eq.4) then

 

   	read(10,*) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q



   	if (id .eq. 129) then 

  	write(20, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

  	elseif (id .eq. 133) then 

  	write(21, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

  	elseif (id .eq. 137) then 

  	write(22, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

  	elseif (id .eq. 141) then 

  	write(23, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

  	elseif (id .eq. 145) then 

  	write(24, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

  	elseif (id .eq. 149) then 

  	write(25, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

  	elseif (id .eq. 153) then 

  	write(26, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bd3, bo4, abo, nlp, q

  	elseif (id .eq. 157) then 

  	write(27, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

  	204 format(8I4, 7f14.3) 

    endif

    

! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.

    write (30, 304)  I, id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q

    304 format(9I4, 7f14.3)



! Corresponding to "if (nb.eq.0) then "

 

  endif

  

! Corresponding to "if (atype .eq. 4) then"

  endif

  

   

  enddo

  

  do L =1,tailline

  read(10,*)

  enddo

  

  enddo

  

  end program main

tools/reax/bonds.reax

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tools/reax/mol_fra.c

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