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rdf_com.f
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program rdf_com
C This program genrerates COM-COM radial distribution using xyz file
C
C Copyright (C) 2019 Oleg N. Starovoytov
C
C Last time updated: Wed Aug 21 12:10:04 JST 2019
C
C This program is free software; you can redistribute it and/or
C modify it under the terms of the GNU General Public License
C as published by the Free Software Foundation; either version 2
C of the License, or (at your option) any later version.
C
C https://www.gnu.org/licenses/quick-guide-gplv3.html
C
C This program is distributed in the hope that it will be useful,
C but WITHOUT ANY WARRANTY; without even the implied warranty of
C MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
C GNU General Public License for more details.
implicit none
integer n
parameter (n=1000000)
integer natm, tatm
integer i_unit, j_unit, k_unit
integer i_type, mol_num(n), atm_num(n)
integer i_count, mol_count, atm_count, mol_type
integer i, j, k, l, m, o, p, q, s, t, u, v, w
integer nfr, num, ig, nbin, g(50,n), i_rdf
real*4 NA, AN
real*4 x(n), y(n), z(n)
real*4 boxAX, boxAY, boxAZ, volume
real*4 atm_mass, sys_mass
real*4 cn(50,n), gr(50,n)
real*4 massX(50,n), massY(50,n), massZ(50,n), massM(50,n)
real*4 xx, yy, zz, r, rdb, bin, vbin, rho, nid, nrho(50)
character*3 ext
character*4 atm_name
character*72 file_name
C
i_unit = 67
j_unit = 68
k_unit = 69
C
ext = 'RDF'
C
NA = 6.02214076E+23
AN = 1E-24
C Redaing 'rdf.par' parameter file
open (i_unit,file='rdf.par',status='old')
read(i_unit,*)
read(i_unit,*) mol_type
read(i_unit,*)
read(i_unit,*) (mol_num(i), i = 1, mol_type)
read(i_unit,*)
read(i_unit,*) (atm_num(j), j = 1, mol_type)
read(i_unit,*)
read(i_unit,*) rdb, nbin
read(i_unit,*)
read(i_unit,*) boxAX, boxAY, boxAZ
close(i_unit)
C Initializing number of bins
do i = 1, mol_type
do j = 1, nbin
g(i,j) = 0
cn(i,j) = 0.0d0
gr(i,j) = 0.0d0
enddo
enddo
C
bin = (rdb/nbin)
C
write(6,*) '-----------------------------------------------------'
write(6,*) 'Distance, Å :', rdb
write(6,*) 'Number of bins:', nbin
write(6,*) 'Bin size, Å :', bin
write(6,*) '-----------------------------------------------------'
C Calculate total number of atoms
natm = 0
do k = 1, mol_type
natm = natm + int(real(mol_num(k)) * real(atm_num(k)))
enddo
C Calculate volume of simulation box
volume = 0.0d0
volume = boxAX * boxAY * boxAZ
C
write(6,*) 'Mol types :', mol_type
write(6,*) 'Num of mols :', (mol_num(i), i = 1, mol_type)
write(6,*) 'Num of atoms :', (atm_num(j), j = 1, mol_type)
write(6,*) 'Total N atoms:', natm
write(6,*) '-----------------------------------------------------'
C Input xyz file
write(6,*) 'Please type the name of your XYZ file.'
read(*,*) file_name
write(6,*) '-----------------------------------------------------'
open (j_unit, file=file_name, status='unknown')
C Initializing number of frames
nfr = 0
34 continue
C Start reading xyz file
read(j_unit,*,end=1289) tatm
read(j_unit,*,end=1289)
C Initializing frame count
nfr = nfr + 1
C Number of atoms in rdf.par file should be equal to the number in xyz file
if (tatm.ne.natm) write(6,*) 'Total number of atoms is wrong! '; exit
C Initialize parameters for calculatin of radial distributions
sys_mass = 0.0d0
i_rdf = 0
i_type = 1
i_count = 1
mol_count = 1
atm_count = 0
C Start reading atomic positions
do l = 1, tatm
read(j_unit,*,end=1289) atm_name, x(l), y(l), z(l)
atm_count = atm_count + 1
if (atm_count.gt.atm_num(i_type)) then
i_count = i_count + 1
mol_count = mol_count + 1
atm_count = 1
endif
if (mol_count.gt.mol_num(i_type)) then
i_type = i_type + 1
mol_count = 1
endif
C Assigning atomic mass and calculating COM coordinates
call assign_name(atm_name, atm_mass)
massX( i_type, mol_count ) =
& massX( i_type, mol_count ) + atm_mass * x(l)
massY( i_type, mol_count ) =
& massY( i_type, mol_count ) + atm_mass * y(l)
massZ( i_type, mol_count ) =
& massZ( i_type, mol_count ) + atm_mass * z(l)
massM( i_type, mol_count ) =
& massM( i_type, mol_count ) + atm_mass
sys_mass = sys_mass + atm_mass
enddo
C Finilizing COM coordinate calculations
do m = 1, i_type
do o = 1, mol_num(m)
massX(m,o) = massX(m,o) / massM(m,o)
massY(m,o) = massY(m,o) / massM(m,o)
massZ(m,o) = massZ(m,o) / massM(m,o)
enddo
enddo
C Start calculations of radial distribution
do s = 1, i_type
do t = 1, i_type
if (t.eq.s.or.t.gt.s) then
i_rdf = i_rdf + 1
do p = 1, mol_num(s)
do q = 1, mol_num(t)
xx = massX(s,p) - massX(t,q)
yy = massY(s,p) - massY(t,q)
zz = massZ(s,p) - massZ(t,q)
C Periodic boundary condition
xx = xx - boxAX * nint( xx / boxAX )
yy = yy - boxAY * nint( yy / boxAY )
zz = zz - boxAZ * nint( zz / boxAZ )
C COM-COM distance
r = sqrt( xx * xx + yy * yy + zz * zz)
if ( r .lt. boxAX / 2.0d0 ) then
if ( r .lt. boxAY / 2.0d0 ) then
if ( r .lt. boxAZ / 2.0d0 ) then
ig = int( r / bin )
if (ig.ne.0) g(i_rdf,ig) = g(i_rdf,ig) + 1
endif
endif
endif
C
enddo
enddo
endif
enddo
enddo
C Clear up COM coordinates for the next frame
do w = 1, i_type
do u = 1, mol_num(w)
massX(w,u) = 0.0d0
massY(w,u) = 0.0d0
massZ(w,u) = 0.0d0
massM(w,u) = 0.0d0
enddo
enddo
C
goto 34
1289 continue
C Calculating the density of a system
rho = (sys_mass / NA) / (volume * AN)
C Print average results of calculations
write(6,*) 'Density, g/cm3:', rho
write(6,*) 'Average Volume, Å3:', volume
write(6,*) 'Number of frames :', nfr
write(6,*) 'Average box size :', boxAX, boxAY, boxAZ
write(6,*) 'System mass :', sys_mass
write(6,*) '-----------------------------------------------------'
C Initializing file for RDF output
call parse_name(file_name, ext, k_unit)
C Calculating radial distributions
call make_rdf(bin, nbin, i_type, i_rdf, nfr, volume, mol_num,
& g, gr, cn)
C Print results of radial calculations to a file
call print_rdf(bin, nbin, i_rdf, gr, cn, k_unit)
write(6,*) 'CLOSING FILE: ', file_name
close(j_unit)
close(k_unit)
C
end
C ------------------------------------------------------------------
C Parsing input filename
subroutine parse_name(file_name, ext, k_unit)
integer i, k_unit, lth
character*(*) file_name, ext
lth = LEN(TRIM(file_name))
do i=1, lth
if (file_name(i:i) == '.') then
open(k_unit, file = file_name(1:i)//ext, status='unknown')
write(6,*) 'OPENING FILE: ', file_name(1:i)//ext
endif
enddo
C
return
C
end
C ------------------------------------------------------------------
C Make rdf
subroutine make_rdf(bin, nbin, i_type, i_rdf, nfr, volume,
& mol_num, g, gr, cn)
C Frenkel, D. and Berend, S.; Understanding MD simulations:
C from algorithms to applications; Chapter 4: Molecular
C dynamics simulations; Academic Press: Elsevier 2007; pp 85-86.
integer n
parameter (n=1000000)
integer i, j, k, nbin, i_type, i_rdf, nfr
integer mol_num(n), k_num(n), g(50,n)
real*4 PI
real*4 r, vbin, nid, bin, volume
real*4 nrho(50), nr(50)
real*4 gr(50,n), cn(50,n)
C
PI = acos(-1.0d0)
i_rdf = 0
C Number density
do i = 1, i_type
do j = 1, i_type
if (j.eq.i.or.j.gt.i) then
i_rdf = i_rdf + 1
nr(i_rdf) = 0.0d0
nrho(i_rdf) = real( (mol_num(j)) / volume )
k_num(i_rdf) = mol_num(i)
endif
enddo
enddo
C Finalizing calculations of radial distributions
do k = 1, i_rdf
do l = 0, nbin
r = bin * ( l + 0.5 )
vbin = ( ( l + 1 )**3 - l**3) * bin**3
nid = ( 4.0d0 / 3.0d0 ) * PI * vbin * nrho(k)
gr(k,l) = real( g(k,l) / ( nfr * k_num(k) * nid ) )
nr(k) = nr(k) + gr(k,l) * nid
cn(k,l) = cn(k,l) + nr(k)
enddo
enddo
end
C ------------------------------------------------------------------
C Print results
subroutine print_rdf(bin, nbin, i_rdf, gr, cn, k_unit)
integer n
parameter (n=1000000)
integer i, j, nbin, i_rdf, k_unit
real*4 bin, r, gr(50,n), cn(50,n)
write(k_unit,*) '#r ',(' gr',i,' cn',i, i = 1, i_rdf)
do j = 0, nbin
r = bin * ( j + 0.5 )
write(k_unit,*) r, (gr(i,j), cn(i,j), i = 1, i_rdf)
enddo
end
C ------------------------------------------------------------------
C Assign proper names to atoms
subroutine assign_name(atm_name, atm_mass)
integer i
real*4 atm_mass
character*4 atm_name
real*4 atom_mass(120)
character*4 atom_name(120)
character*1 name_1
character*2 name_2
character*3 name_3
character*4 name_4
C -----------------------------------------------------------------
C Chemical elements of the periodic table, atomic mass (a.u.).
C
atom_mass(1) = 1.0079 ! H
atom_mass(2) = 4.0026 ! He
atom_mass(3) = 6.9410 ! Li
atom_mass(4) = 9.0122 ! Be
atom_mass(5) = 10.8110 ! B
atom_mass(6) = 12.0107 ! C
atom_mass(7) = 14.0067 ! N
atom_mass(8) = 15.9994 ! O
atom_mass(9) = 18.9984 ! F
atom_mass(10) = 20.1797 ! Ne
atom_mass(11) = 22.9897 ! Na
atom_mass(12) = 24.3050 ! Mg
atom_mass(13) = 26.9815 ! Al
atom_mass(14) = 28.0855 ! Si
atom_mass(15) = 30.9738 ! P
atom_mass(16) = 32.0650 ! S
atom_mass(17) = 35.4530 ! Cl
atom_mass(18) = 39.0983 ! K
atom_mass(19) = 39.9480 ! Ar
atom_mass(20) = 40.0780 ! Ca
atom_mass(21) = 44.9559 ! Sc
atom_mass(22) = 47.8670 ! Ti
atom_mass(23) = 50.9415 ! V
atom_mass(24) = 51.9961 ! Cr
atom_mass(25) = 54.9380 ! Mn
atom_mass(26) = 55.8450 ! Fe
atom_mass(27) = 58.6934 ! Ni
atom_mass(28) = 58.9332 ! Co
atom_mass(29) = 63.5460 ! Cu
atom_mass(30) = 65.3900 ! Zn
atom_mass(31) = 69.7230 ! Ga
atom_mass(32) = 72.6400 ! Ge
atom_mass(33) = 74.9216 ! As
atom_mass(34) = 78.9600 ! Se
atom_mass(35) = 79.9040 ! Br
atom_mass(36) = 83.8000 ! Kr
atom_mass(37) = 85.4678 ! Ru
atom_mass(38) = 87.6200 ! St
atom_mass(39) = 88.9059 ! Y
atom_mass(40) = 91.2240 ! Zr
atom_mass(41) = 92.9064 ! Nb
atom_mass(42) = 95.9400 ! Mo
atom_mass(43) = 98.0000 ! Tc
atom_mass(44) = 101.070 ! Ru
atom_mass(45) = 102.9055 ! Rh
atom_mass(46) = 106.4200 ! Pd
atom_mass(47) = 107.8682 ! Ag
atom_mass(48) = 112.4110 ! Cd
atom_mass(49) = 114.8180 ! In
atom_mass(50) = 118.7100 ! Sn
atom_mass(51) = 121.7600 ! Sb
atom_mass(52) = 126.9045 ! I
atom_mass(53) = 127.6000 ! Te
atom_mass(54) = 131.2930 ! Xe
atom_mass(55) = 132.9055 ! Cs
atom_mass(56) = 137.3270 ! Ba
atom_mass(57) = 138.9055 ! La
atom_mass(58) = 140.1160 ! Ce
atom_mass(59) = 140.9077 ! Pr
atom_mass(60) = 144.2400 ! Nd
atom_mass(61) = 145.0000 ! Pm
atom_mass(62) = 150.3600 ! Sm
atom_mass(63) = 151.9640 ! Eu
atom_mass(64) = 157.2500 ! Gd
atom_mass(65) = 158.9253 ! Tb
atom_mass(66) = 162.5000 ! Dy
atom_mass(67) = 164.9303 ! Ho
atom_mass(68) = 167.2590 ! Er
atom_mass(69) = 168.9342 ! Tm
atom_mass(70) = 173.0400 ! Yb
atom_mass(71) = 174.9670 ! Lu
atom_mass(72) = 178.4900 ! Hf
atom_mass(73) = 180.9479 ! Ta
atom_mass(74) = 183.8400 ! W
atom_mass(75) = 186.2070 ! Re
atom_mass(76) = 190.2300 ! Os
atom_mass(77) = 192.2170 ! Ir
atom_mass(78) = 195.0780 ! Pt
atom_mass(79) = 196.9665 ! Au
atom_mass(80) = 200.5900 ! Hg
atom_mass(81) = 204.3833 ! Ti
atom_mass(82) = 207.2000 ! Pb
atom_mass(83) = 208.9804 ! Bi
atom_mass(84) = 209.0000 ! Po
atom_mass(85) = 210.0000 ! At
atom_mass(86) = 222.0000 ! Rn
atom_mass(87) = 223.0000 ! Fr
atom_mass(88) = 226.0000 ! Ra
atom_mass(89) = 227.0000 ! Ac
atom_mass(90) = 231.0359 ! Pa
atom_mass(91) = 232.0381 ! Th
atom_mass(92) = 237.0000 ! Np
atom_mass(93) = 238.0289 ! U
atom_mass(94) = 243.0000 ! Am
atom_mass(95) = 244.0000 ! Pu
atom_mass(96) = 247.0000 ! Cm
atom_mass(97) = 247.0000 ! Bk
atom_mass(98) = 251.0000 ! Cf
atom_mass(99) = 252.0000 ! Es
atom_mass(100) = 257.0000 ! Fm
atom_mass(101) = 258.0000 ! Md
atom_mass(102) = 259.0000 ! No
atom_mass(103) = 261.0000 ! Rf
atom_mass(104) = 262.0000 ! Lr
atom_mass(105) = 262.0000 ! Db
atom_mass(106) = 264.0000 ! Bh
atom_mass(107) = 266.0000 ! Sg
atom_mass(108) = 268.0000 ! Mt
atom_mass(109) = 272.0000 ! Rg
atom_mass(110) = 277.0000 ! Hs
atom_mass(111) = 0.0000 ! Ds
atom_mass(112) = 0.0000 ! Uub
atom_mass(113) = 0.0000 ! Uut
atom_mass(114) = 0.0000 ! Uuq
atom_mass(115) = 0.0000 ! Uup
atom_mass(116) = 0.0000 ! Uuh
atom_mass(117) = 0.0000 ! Uus
atom_mass(118) = 0.0000 ! Uuo
atom_mass(119) = 0.0000 ! ---
atom_mass(120) = 0.0000 ! ---
C -----------------------------------------------------------------
C Chemical elements of the periodic table, atom names
atom_name(1) = 'H'
atom_name(2) = 'He'
atom_name(3) = 'Li'
atom_name(4) = 'Be'
atom_name(5) = 'B'
atom_name(6) = 'C'
atom_name(7) = 'N'
atom_name(8) = 'O'
atom_name(9) = 'F'
atom_name(10) = 'Ne'
atom_name(11) = 'Na'
atom_name(12) = 'Mg'
atom_name(13) = 'Al'
atom_name(14) = 'Si'
atom_name(15) = 'P'
atom_name(16) = 'S'
atom_name(17) = 'Cl'
atom_name(18) = 'K'
atom_name(19) = 'Ar'
atom_name(20) = 'Ca'
atom_name(21) = 'Sc'
atom_name(22) = 'Ti'
atom_name(23) = 'V'
atom_name(24) = 'Cr'
atom_name(25) = 'Mn'
atom_name(26) = 'Fe'
atom_name(27) = 'Ni'
atom_name(28) = 'Co'
atom_name(29) = 'Cu'
atom_name(30) = 'Zn'
atom_name(31) = 'Ga'
atom_name(32) = 'Ge'
atom_name(33) = 'As'
atom_name(34) = 'Se'
atom_name(35) = 'Br'
atom_name(36) = 'Kr'
atom_name(37) = 'Ru'
atom_name(38) = 'St'
atom_name(39) = 'Y'
atom_name(40) = 'Zr'
atom_name(41) = 'Nb'
atom_name(42) = 'Mo'
atom_name(43) = 'Tc'
atom_name(44) = 'Ru'
atom_name(45) = 'Rh'
atom_name(46) = 'Pd'
atom_name(47) = 'Ag'
atom_name(48) = 'Cd'
atom_name(49) = 'In'
atom_name(50) = 'Sn'
atom_name(51) = 'Sb'
atom_name(52) = 'I'
atom_name(53) = 'Te'
atom_name(54) = 'Xe'
atom_name(55) = 'Cs'
atom_name(56) = 'Ba'
atom_name(57) = 'La'
atom_name(58) = 'Ce'
atom_name(59) = 'Pr'
atom_name(60) = 'Nd'
atom_name(61) = 'Pm'
atom_name(62) = 'Sm'
atom_name(63) = 'Eu'
atom_name(64) = 'Gd'
atom_name(65) = 'Tb'
atom_name(66) = 'Dy'
atom_name(67) = 'Ho'
atom_name(68) = 'Er'
atom_name(69) = 'Tm'
atom_name(70) = 'Yb'
atom_name(71) = 'Lu'
atom_name(72) = 'Hf'
atom_name(73) = 'Ta'
atom_name(74) = 'W'
atom_name(75) = 'Re'
atom_name(76) = 'Os'
atom_name(77) = 'Ir'
atom_name(78) = 'Pt'
atom_name(79) = 'Au'
atom_name(80) = 'Hg'
atom_name(81) = 'Ti'
atom_name(82) = 'Pb'
atom_name(83) = 'Bi'
atom_name(84) = 'Po'
atom_name(85) = 'At'
atom_name(86) = 'Rn'
atom_name(87) = 'Fr'
atom_name(88) = 'Ra'
atom_name(89) = 'Ac'
atom_name(90) = 'Pa'
atom_name(91) = 'Th'
atom_name(92) = 'Np'
atom_name(93) = 'U'
atom_name(94) = 'Am'
atom_name(95) = 'Pu'
atom_name(96) = 'Cm'
atom_name(97) = 'Bk'
atom_name(98) = 'Cf'
atom_name(99) = 'Es'
atom_name(100) = 'Fm'
atom_name(101) = 'Md'
atom_name(102) = 'No'
atom_name(103) = 'Rf'
atom_name(104) = 'Lr'
atom_name(105) = 'Db'
atom_name(106) = 'Bh'
atom_name(107) = 'Sg'
atom_name(108) = 'Mt'
atom_name(109) = 'Rg'
atom_name(110) = 'Hs'
atom_name(111) = 'Ds'
atom_name(112) = 'Uub'
atom_name(113) = 'Uut'
atom_name(114) = 'Uuq'
atom_name(115) = 'Uup'
atom_name(116) = 'Uuh'
atom_name(117) = 'Uus'
atom_name(118) = 'Uuo'
atom_name(119) = 'NAY'
atom_name(120) = 'NAY'
name_1 = atm_name
name_2 = atm_name
name_3 = atm_name
name_4 = atm_name
do i = 1, 120
if ( name_1 == atom_name(i) ) atm_name = atom_name(i)
if ( name_2 == atom_name(i) ) atm_name = atom_name(i)
if ( name_3 == atom_name(i) ) atm_name = atom_name(i)
if ( name_4 == atom_name(i) ) atm_name = atom_name(i)
if ( name_1 == atom_name(i) ) atm_mass = atom_mass(i)
if ( name_2 == atom_name(i) ) atm_mass = atom_mass(i)
if ( name_3 == atom_name(i) ) atm_mass = atom_mass(i)
if ( name_4 == atom_name(i) ) atm_mass = atom_mass(i)
enddo
end