-
Notifications
You must be signed in to change notification settings - Fork 1
/
rdf.cpp
114 lines (94 loc) · 4.38 KB
/
rdf.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
/* This Code analyzes trajectories from MD Simulations Using Gromacs
* Trajectory data is saved in XTC files
* Outpus radial distribution functions
* by Suruchi Fialoke
*/
#include <cmath>
#include <cstdlib>
#include <iostream>
#include <cstring>
#include <fstream>
#include <ctime>
#include <malloc.h>
#include </opt/gromacs/4.5.5/include/xdrfile/xdrfile_xtc.h> // xdr include file locations
using namespace std;
int main(int argc, char **argv) {
/* XTC variables */
XDRFILE *xd; // the xdr file holder
int natoms=0; // number of atoms
int step; // the step counter for the simulation
float time; // simulation time
matrix box; // box coordinates in a 3x3 matrix
rvec *xtc_coor; // atom coordinates in a 2-D matrix
float prec; // precision of the xtc file
cout<<"******* 3D g(r) of water(NVT, 20ns)*********\n";
/* Program variables */
int num_water= 4000 ; //number of water in the simulation box
float L = 5.0 ; //box length
int firstsnap,lastsnap ; //first and last snapshots to loop
cout<<"Enter first time snap\n";
cin>>firstsnap ;
cout<<"Enter last time snap\n";
cin>>lastsnap ;
int snap_num = 0 ; //accounts for the frame that is being looped
int snap_count = 0 ; // accounts from the frames that are counted
int oxy_in_frame = 0 ; //keeps a track of # of oxygen counted
int n_bins = 1000 ; // number of bins in the histogram
float dr = 0.5*L/n_bins ; //delta r for increments in r
double g_r[n_bins] ; // g(r) stores # in each bin
float rho_bulk = num_water/(L*L*L) ; // bulk density
double rij,rijsq,dx,dy,dz ; //variables for instantaneous rij calculations
/* End of Program variables */
for(int k=0;k<n_bins;k++)
{
g_r[k] = 0;
}
/* Memory allocation to read coordinates */
read_xtc_natoms(argv[1], &natoms);
xtc_coor = (rvec *) malloc(natoms*sizeof(rvec));
if(xtc_coor==0)
{
cout<<"Insufficient memory to load .xtc file.\n";
return 0;
}
/* Open the xtc file and loop through each frame. */
xd=xdrfile_open(argv[1],"r");
while( ! read_xtc(xd, natoms, &step, &time, box, xtc_coor, &prec) )
{
snap_num++ ;
if((snap_num>firstsnap)&&(snap_num<lastsnap))
{
snap_count++ ;
oxy_in_frame = 0 ;
for (int i=0; i<num_water -1; i++)
{
for (int j=i+1; j<num_water; j++)
{ /*Correcting for Periodic Boindary Conditions to calculate distances*/
dx = (xtc_coor[3*i][0]-xtc_coor[3*j][0]) ;
dx = dx - L*round(dx/L);
dy = (xtc_coor[3*i][1]-xtc_coor[3*j][1]) ;
dy = dy - L*round(dy/L);
dz = (xtc_coor[3*i][2]-xtc_coor[3*j][2]) ;
dz = dz - L*round(dz/L);
rijsq = dx*dx+dy*dy+dz*dz ;
rij=sqrt(rijsq) ;
if(rij<0.5*L){
g_r[(int)(rij/dr)] += 2.0;
oxy_in_frame++ ;
}
}
}
}
}
if(step==0) {
cout<<step<<"\t"<<natoms<<endl;
cout<<box[0][0]<<"\t"<<box[1][1]<<"\t"<<box[2][2]<<endl;
}
for(int k=0;k<n_bins;k++)
{
g_r[k] /= snap_count*num_water;
g_r[k] /= 4.0*M_PI*k*k*pow(dr,3)*rho_bulk;
cout<<dr*(k+0.5)<<"\t"<<g_r[k]<<endl;
}
return 0 ;
}