void ReadWrite(char *rfile, char *wfile, int in_xtcBool, int out_xtcBool, int in_trrBool, int out_trrBool)
{
XDRFILE *xd_read, *xd_write;
int result_xtc, result_trr;
int natoms_xtc, natoms_trr;
int step_xtc, step_trr;
float time_xtc, time_trr;
matrix box_xtc, box_trr;
rvec *x_xtc, *x_trr, *v_trr, *f_trr;
float prec_xtc = 1000.0;
float lambda_trr = 0.0;
xd_read = xdrfile_open(rfile, "r");
if (NULL == xd_read)
die("Opening xdrfile for reading");
/* Test whether output file exists */
if ((xd_write = xdrfile_open(wfile,"r")) != NULL) {
xdrfile_close(xd_write);
die("Output file exists.");
}
/* Output file does not exist. Now we can open it for writing */
xd_write = xdrfile_open(wfile, "w");
if (NULL == xd_write)
die("Opening xdrfile for writing");
/* .xtc -> .xtc */
if(in_xtcBool && out_xtcBool)
{
result_xtc = read_xtc_natoms(rfile, &natoms_xtc);
if (exdrOK != result_xtc)
die_r("read_xtc_natoms",result_xtc);
x_xtc = (rvec *)calloc(natoms_xtc, sizeof(x_xtc[0]));
while(1)
{
result_xtc = read_xtc(xd_read, natoms_xtc, &step_xtc, &time_xtc,
box_xtc, x_xtc, &prec_xtc);
if (result_xtc == 0) // if not reach the end of file, write it to the output.xtc file
{
if (exdrOK != result_xtc)
die_r("Reading xtc file", result_xtc);
result_xtc = write_xtc(xd_write, natoms_xtc, step_xtc, time_xtc,
box_xtc, x_xtc, prec_xtc);
if (result_xtc != 0)
die_r("Writing xtc file", result_xtc);
}
else
break;
}
}
/* .xtc -> .trr */
if(in_xtcBool && out_trrBool)
{
result_xtc = read_xtc_natoms(rfile, &natoms_xtc);
if (exdrOK != result_xtc)
die_r("read_xtc_natoms",result_xtc);
x_xtc = (rvec *)calloc(natoms_xtc, sizeof(x_xtc[0]));
while(1)
{
result_xtc = read_xtc(xd_read, natoms_xtc, &step_xtc, &time_xtc,
box_xtc, x_xtc, &prec_xtc);
if (result_xtc == 0) // if not reach the end of file, write it to the output.trr file
{
if (exdrOK != result_xtc)
die_r("Reading xtc file", result_xtc);
result_trr = write_trr(xd_write, natoms_xtc, step_xtc, time_xtc, lambda_trr,
box_xtc, x_xtc, NULL, NULL);
if (0 != result_trr)
die_r("Writing trr file",result_trr);
}
else
break;
}
}
/* .trr -> .trr */
if(in_trrBool && out_trrBool)
{
result_trr = read_trr_natoms(rfile, &natoms_trr);
if (exdrOK != result_trr)
die_r("read_trr_natoms",result_trr);
x_trr = (rvec *)calloc(natoms_trr, sizeof(x_trr[0]));
v_trr = (rvec *)calloc(natoms_trr, sizeof(v_trr[0]));
f_trr = (rvec *)calloc(natoms_trr, sizeof(f_trr[0]));
while (1)
{
result_trr = read_trr(xd_read, natoms_trr, &step_trr, &time_trr, &lambda_trr,
box_trr, x_trr, v_trr, f_trr);
int ii_trr, jj_trr, x_ck=0, v_ck=0, f_ck=0;
int x_ck_bool=0, v_ck_bool=0, f_ck_bool=0;
for (ii_trr = 0; ii_trr < natoms_trr; ii_trr++)
{
for(jj_trr = 0; jj_trr < DIM; jj_trr++)
{
if (x_trr[ii_trr][jj_trr] == 0)
x_ck++;
if (v_trr[ii_trr][jj_trr] == 0)
v_ck++;
if (f_trr[ii_trr][jj_trr] == 0)
f_ck++;
}
}
if (x_ck == natoms_trr*DIM)
x_ck_bool = 1;
if (v_ck == natoms_trr*DIM)
v_ck_bool = 1;
if (f_ck == natoms_trr*DIM)
f_ck_bool = 1;
if (result_trr == 0) // if not reach the end of file, write it to the output.trr file
{
if (exdrOK != result_trr)
die_r("Reading trr file",result_trr);
if(v_ck_bool && f_ck_bool)
result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr,
box_trr, x_trr, NULL, NULL);
else if(v_ck_bool)
result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr,
box_trr, x_trr, NULL, f_trr);
else if(f_ck_bool)
result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr,
box_trr, x_trr, v_trr, NULL);
else
result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr,
box_trr, x_trr, v_trr, f_trr);
if (0 != result_trr)
die_r("Writing trr file",result_trr);
}
else
break;
}
}
/* .trr -> .xtc */
if(in_trrBool && out_xtcBool)
{
result_trr = read_trr_natoms(rfile, &natoms_trr);
if (exdrOK != result_trr)
die_r("read_trr_natoms",result_trr);
x_trr = (rvec *)calloc(natoms_trr, sizeof(x_trr[0]));
v_trr = (rvec *)calloc(natoms_trr, sizeof(v_trr[0]));
f_trr = (rvec *)calloc(natoms_trr, sizeof(f_trr[0]));
while(1)
{
result_trr = read_trr(xd_read, natoms_trr, &step_trr, &time_trr, &lambda_trr,
box_trr, x_trr, v_trr, f_trr);
if (result_trr == 0) // if not reach the end of file, write it to the output.trr file
{
if (exdrOK != result_trr)
die_r("Reading trr file", result_trr);
result_xtc = write_xtc(xd_write, natoms_trr, step_trr, time_trr,
box_trr, x_trr, prec_xtc);
if (result_xtc != 0)
die_r("Writing xtc file", result_xtc);
}
else
break;
}
}
xdrfile_close(xd_read);
xdrfile_close(xd_write);
}
static void test_trr()
{
char *testfn = "test.trr";
XDRFILE *xd;
int result,i,j,k,nframes=13;
int natoms2,natoms1=173;
int step2,step1=1993;
float time2,time1=1097.23;
matrix box2,box1;
rvec *x2,*x1;
float lambda2,lambda1=0.4;
float toler=1e-3;
printf("Testing trr functionality:");
for(i=0; (i<DIM); i++)
for(j=0; (j<DIM); j++)
box1[i][j] = (i+1)*3.7 + (j+1);
x1 = calloc(natoms1,sizeof(*x1));
if (NULL == x1)
die("Allocating memory for x1 in test_xtc");
for(i=0; (i<natoms1); i++)
for(j=0; (j<DIM); j++)
x1[i][j] = (i+1)*3.7 + (j+1);
xd = xdrfile_open(testfn,"w");
if (NULL == xd)
die("Opening trr file for writing");
for(k=0; (k<nframes); k++)
{
result = write_trr(xd,natoms1,step1+k,time1+k,lambda1,box1,x1,NULL,NULL);
if (0 != result)
die_r("Writing trr file",result);
}
xdrfile_close(xd);
result = read_trr_natoms(testfn,&natoms2);
if (exdrOK != result)
die_r("read_trr_natoms",result);
if (natoms2 != natoms1)
die("Number of atoms incorrect when reading trr");
x2 = calloc(natoms2,sizeof(x2[0]));
if (NULL == x2)
die("Allocating memory for x2");
xd = xdrfile_open(testfn,"r");
if (NULL == xd)
die("Opening trr file for reading");
for(k=0; (k<nframes); k++)
{
result = read_trr(xd,natoms2,&step2,&time2,&lambda2,box2,x2,NULL,NULL);
if (exdrOK != result)
die_r("read_xtc",result);
if (natoms2 != natoms1)
die("natoms2 != natoms1");
if (step2-step1 != k)
die("incorrect step");
if (fabs(time2-time1-k) > toler)
die("incorrect time");
if (fabs(lambda2-lambda2) > toler)
die("incorrect lambda");
for(i=0; (i<DIM); i++)
for(j=0; (j<DIM); j++)
if (fabs(box2[i][j] - box1[i][j]) > toler)
die("box incorrect");
for(i=0; (i<natoms1); i++)
for(j=0; (j<DIM); j++)
if (fabs(x2[i][j] - x1[i][j]) > toler)
die("x incorrect");
}
xdrfile_close(xd);
#ifdef HAVE_UNISTD
unlink(testfn);
#endif
printf(" PASSED\n");
}
