#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-typedef struct {
- char *label;
+typedef struct
+{
+ char* label;
int cg;
real q;
} t_charge;
-static t_charge *mk_charge(const t_atoms *atoms, int *nncg)
+static t_charge* mk_charge(const t_atoms* atoms, int* nncg)
{
- t_charge *cg = nullptr;
+ t_charge* cg = nullptr;
char buf[32];
int i, ncg, resnr, anr;
real qq;
qq = atoms->atom[i].q;
if (std::abs(qq) > 1.0e-5)
{
- srenew(cg, ncg+1);
+ srenew(cg, ncg + 1);
cg[ncg].q = qq;
cg[ncg].cg = i;
anr = i;
resnr = atoms->atom[anr].resind;
- sprintf(buf, "%s%d-%d",
- *(atoms->resinfo[resnr].name),
- atoms->resinfo[resnr].nr,
- anr+1);
+ sprintf(buf, "%s%d-%d", *(atoms->resinfo[resnr].name), atoms->resinfo[resnr].nr, anr + 1);
cg[ncg].label = gmx_strdup(buf);
ncg++;
}
for (i = 0; (i < ncg); i++)
{
- printf("CG: %10s Q: %6g Atoms:",
- cg[i].label, cg[i].q);
+ printf("CG: %10s Q: %6g Atoms:", cg[i].label, cg[i].q);
printf(" %4d", cg[i].cg);
printf("\n");
}
return cg;
}
-int gmx_saltbr(int argc, char *argv[])
+int gmx_saltbr(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] plots the distance between all combination of charged groups",
"as a function of time. The groups are combined in different ways.",
"A minimum distance can be given (i.e. a cut-off), such that groups",
"that are never closer than that distance will not be plotted.[PAR]",
"Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
"and [TT]plus-plus.xvg[tt], or files for every individual ion pair if the [TT]-sep[tt]",
- "option is selected. In this case, files are named as [TT]sb-(Resname)(Resnr)-(Atomnr)[tt].",
+ "option is selected. In this case, files are named as ",
+ "[TT]sb-(Resname)(Resnr)-(Atomnr)[tt].",
"There may be [BB]many[bb] such files."
};
static gmx_bool bSep = FALSE;
static real truncate = 1000.0;
- t_pargs pa[] = {
- { "-t", FALSE, etREAL, {&truncate},
- "Groups that are never closer than this distance are not plotted" },
- { "-sep", FALSE, etBOOL, {&bSep},
- "Use separate files for each interaction (may be MANY)" }
- };
- t_filenm fnm[] = {
- { efTRX, "-f", nullptr, ffREAD },
- { efTPR, nullptr, nullptr, ffREAD },
+ t_pargs pa[] = { { "-t",
+ FALSE,
+ etREAL,
+ { &truncate },
+ "Groups that are never closer than this distance are not plotted" },
+ { "-sep",
+ FALSE,
+ etBOOL,
+ { &bSep },
+ "Use separate files for each interaction (may be MANY)" } };
+ t_filenm fnm[] = {
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
};
#define NFILE asize(fnm)
- FILE *out[3], *fp;
- static const char *title[3] = {
- "Distance between positively charged groups",
- "Distance between negatively charged groups",
- "Distance between oppositely charged groups"
- };
- static const char *fn[3] = {
- "plus-plus.xvg",
- "min-min.xvg",
- "plus-min.xvg"
- };
- int nset[3] = {0, 0, 0};
+ FILE * out[3], *fp;
+ static const char* title[3] = { "Distance between positively charged groups",
+ "Distance between negatively charged groups",
+ "Distance between oppositely charged groups" };
+ static const char* fn[3] = { "plus-plus.xvg", "min-min.xvg", "plus-min.xvg" };
+ int nset[3] = { 0, 0, 0 };
- t_topology *top;
- int ePBC;
- char *buf;
- t_trxstatus *status;
- int i, j, k, m, nnn, teller, ncg;
- real t, *time, qi, qj;
- t_charge *cg;
- real ***cgdist;
- int **nWithin;
+ t_topology* top;
+ int ePBC;
+ char* buf;
+ t_trxstatus* status;
+ int i, j, k, m, nnn, teller, ncg;
+ real t, *time, qi, qj;
+ t_charge* cg;
+ real*** cgdist;
+ int** nWithin;
- t_pbc pbc;
- rvec *x;
- matrix box;
- gmx_output_env_t *oenv;
+ t_pbc pbc;
+ rvec* x;
+ matrix box;
+ gmx_output_env_t* oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc,
+ 0, nullptr, &oenv))
{
return 0;
}
time = nullptr;
do
{
- srenew(time, teller+1);
+ srenew(time, teller + 1);
time[teller] = t;
set_pbc(&pbc, ePBC, box);
for (i = 0; (i < ncg); i++)
{
- for (j = i+1; (j < ncg); j++)
+ for (j = i + 1; (j < ncg); j++)
{
- srenew(cgdist[i][j], teller+1);
+ srenew(cgdist[i][j], teller + 1);
rvec dx;
pbc_dx(&pbc, x[cg[i].cg], x[cg[j].cg], dx);
cgdist[i][j][teller] = norm(dx);
}
teller++;
- }
- while (read_next_x(oenv, status, &t, x, box));
+ } while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
close_trx(status);
snew(buf, 256);
for (i = 0; (i < ncg); i++)
{
- for (j = i+1; (j < ncg); j++)
+ for (j = i + 1; (j < ncg); j++)
{
if (nWithin[i][j])
{
for (i = 0; (i < ncg); i++)
{
qi = cg[i].q;
- for (j = i+1; (j < ncg); j++)
+ for (j = i + 1; (j < ncg); j++)
{
qj = cg[j].q;
if (nWithin[i][j])
{
sprintf(buf, "%s:%s", cg[i].label, cg[j].label);
- if (qi*qj < 0)
+ if (qi * qj < 0)
{
nnn = 2;
}
- else if (qi+qj > 0)
+ else if (qi + qj > 0)
{
nnn = 0;
}
}
}
nset[nnn]++;
- nWithin[i][j] = nnn+1;
+ nWithin[i][j] = nnn + 1;
}
}
}
for (i = 0; (i < ncg); i++)
{
- for (j = i+1; (j < ncg); j++)
+ for (j = i + 1; (j < ncg); j++)
{
nnn = nWithin[i][j];
if (nnn > 0)
{
- fprintf(out[nnn-1], " %10g", cgdist[i][j][k]);
+ fprintf(out[nnn - 1], " %10g", cgdist[i][j][k]);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff