t_pdbfile **pdbf = NULL;
int npdbf;
- parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
- NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
+ NULL, &oenv))
+ {
+ return 0;
+ }
fp = ffopen(opt2fn("-g", NFILE, fnm), "w");
please_cite(stdout, "Hetenyi2002b");
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
indexfile = ftp2fn_null(efNDX, NFILE, fnm);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
acfile = opt2fn_null("-ac", NFILE, fnm);
msdfile = opt2fn_null("-msd", NFILE, fnm);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
+ &oenv))
+ {
+ return 0;
+ }
mult = 4;
maxang = 360.0;
double sum_histrange_err = 0.; /* histogram range error */
double stat_err = 0.; /* statistical error */
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (opt2bSet("-f", NFILE, fnm))
{
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
+ &oenv))
+ {
+ return 0;
+ }
if (bAverDist)
{
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
+ &oenv))
+ {
+ return 0;
+ }
/* Handle result from enumerated type */
sscanf(maxchistr[0], "%d", &maxchi);
if (m->n1 != m->nn)
{
- fprintf(stderr,"Can not do Monte Carlo optimization with a non-square matrix.\n");
+ fprintf(stderr, "Can not do Monte Carlo optimization with a non-square matrix.\n");
return;
}
printf("\nDoing Monte Carlo optimization to find the smoothest trajectory\n");
iswap = jswap = -1;
enorm = m->mat[0][0];
- for(i = 0; (i < m->n1); i++)
+ for (i = 0; (i < m->n1); i++)
{
- for(j = 0; (j < m->nn); j++)
+ for (j = 0; (j < m->nn); j++)
{
- if (m->mat[i][j] > enorm)
+ if (m->mat[i][j] > enorm)
{
- enorm = m->mat[i][j];
+ enorm = m->mat[i][j];
iswap = i;
jswap = j;
}
enorm, iswap, jswap, emin);
rng = gmx_rng_init(seed);
- nn = m->nn;
+ nn = m->nn;
/* Initiate and store global minimum */
- minimum = init_mat(nn, m->b1D);
+ minimum = init_mat(nn, m->b1D);
minimum->nn = nn;
copy_t_mat(minimum, m);
fprintf(log, "Global minimum energy %g\n", mat_energy(minimum));
fprintf(log, "Global minimum energy %g\n", mat_energy(m));
fprintf(log, "Swapped time and frame indices and RMSD to next neighbor:\n");
- for(i=0; (i<m->nn); i++)
+ for (i = 0; (i < m->nn); i++)
{
fprintf(log, "%10g %5d %10g\n",
time[m->m_ind[i]],
m->m_ind[i],
- (i<m->nn-1) ? m->mat[m->m_ind[i]][m->m_ind[i+1]] : 0);
+ (i < m->nn-1) ? m->mat[m->m_ind[i]][m->m_ind[i+1]] : 0);
}
if (NULL != fp)
rvec *xtps, *usextps, *x1, **xx = NULL;
const char *fn, *trx_out_fn;
t_clusters clust;
- t_mat *rms, *orig=NULL;
+ t_mat *rms, *orig = NULL;
real *eigenvalues;
t_topology top;
int ePBC;
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
- &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
+ &oenv))
+ {
+ return 0;
+ }
/* parse options */
bReadMat = opt2bSet("-dm", NFILE, fnm);
ffclose(fp);
break;
case m_monte_carlo:
- orig = init_mat(rms->nn, FALSE);
+ orig = init_mat(rms->nn, FALSE);
orig->nn = rms->nn;
copy_t_mat(orig, rms);
- mc_optimize(log, rms, time, niter, nrandom, seed, kT,
- opt2fn_null("-conv",NFILE,fnm), oenv);
+ mc_optimize(log, rms, time, niter, nrandom, seed, kT,
+ opt2fn_null("-conv", NFILE, fnm), oenv);
break;
case m_jarvis_patrick:
jarvis_patrick(rms->nn, rms->mat, M, P, bJP_RMSD ? rmsdcut : -1, &clust);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
rgblo.r = rlo[XX], rgblo.g = rlo[YY], rgblo.b = rlo[ZZ];
real *msds;
- parse_common_args(&argc, argv, PCA_BE_NICE | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
matchndxfile = opt2fn_null("-no", NFILE, fnm);
conf1file = ftp2fn(efTPS, NFILE, fnm);
conf2file = ftp2fn(efSTX, NFILE, fnm);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
clear_mat(zerobox);
/* At first the arguments will be parsed and the system information processed */
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bACF = opt2bSet("-caf", NFILE, fnm);
bINT = opt2bSet("-mc", NFILE, fnm);
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
+ &oenv))
+ {
+ return 0;
+ }
if (bSymmetrize && !bCenter)
{
npargs = asize(pa);
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bXmin = opt2parg_bSet("-xmin", npargs, pa);
bXmax = opt2parg_bSet("-xmax", npargs, pa);
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
eMeth = nenum(meth);
"Number of points for smoothing" }
};
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
please_cite(stdout, "Spoel98a");
printf("WARNING: non-polarizable models can never yield an infinite\n"
"dielectric constant that is different from 1. This is incorrect\n"
};
real mu_max = 5, mu_aver = -1, rcmax = 0;
real epsilonRF = 0.0, temp = 300;
- gmx_bool bPairs = TRUE, bPhi = FALSE, bQuad = FALSE;
+ gmx_bool bPairs = TRUE, bPhi = FALSE, bQuad = FALSE;
const char *corrtype[] = {NULL, "none", "mol", "molsep", "total", NULL};
const char *axtitle = "Z";
int nslices = 10; /* nr of slices defined */
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
printf("Using %g as mu_max and %g as the dipole moment.\n",
mu_max, mu_aver);
#define NFILE asize(fnm)
cr = init_par();
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, FALSE, 0, &fplog);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bCutoff = opt2parg_bSet("-dist", NPA, pa);
cut2 = cut*cut;
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fnSCount = opt2fn("-sc", NFILE, fnm);
fnArea = opt2fn_null("-a", NFILE, fnm);
fnTArea = opt2fn_null("-ta", NFILE, fnm);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc,
- asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc,
+ asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
beta = 1/(Temp*BOLTZ);
if (bDump)
rrange, krange, rincr, kincr, Rfrac;
int rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
- parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* Check command line options for filenames and set bool flags when switch used*/
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
get_stx_coordnum (opt2fn("-f", NFILE, fnm), &natoms);
init_t_atoms(&atoms, natoms, TRUE);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
bMead = opt2bSet("-mead", NFILE, fnm);
"Stop on errors in the file" }
};
- parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa),
- pa, asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa),
+ pa, asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
tadjust = 0;
nremax = 0;
nset = 0;
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
for (i = 0; (i < egNR+egSP); i++)
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bDRAll = opt2bSet("-pairs", NFILE, fnm);
bDisRe = opt2bSet("-viol", NFILE, fnm) || bDRAll;
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
highfile = opt2fn_null("-oh", NFILE, fnm);
if (highfile)
}
static void mk_vdw(t_atoms *a, real rvdw[], gmx_atomprop_t aps,
- real r_distance,real r_scale)
+ real r_distance, real r_scale)
{
int i;
{
rvdw[i] = r_distance;
}
- else
+ else
{
rvdw[i] *= r_scale;
}
static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
- gmx_atomprop_t aps,
+ gmx_atomprop_t aps,
real r_distance, real r_scale, real rshell,
const output_env_t oenv,
const char* posfn, const rvec deltaR, int enum_rot,
static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **r,
int ePBC, matrix box,
- gmx_atomprop_t aps,
+ gmx_atomprop_t aps,
real r_distance, real r_scale, int *atoms_added,
int *residues_added, real rshell, int max_sol,
const output_env_t oenv)
"Avoid momory leaks during neighbor searching with option -ci. May be slow for large systems." },
};
- parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
bInsert = opt2bSet("-ci", NFILE, fnm) && ((nmol_ins > 0) || opt2bSet("-ip", NFILE, fnm));
bSol = opt2bSet("-cs", NFILE, fnm);
if (bInsert)
{
title_ins = insert_mols(opt2fn("-ci", NFILE, fnm), nmol_ins, nmol_try, seed,
- &atoms, &x, &r, ePBC, box, aps,
+ &atoms, &x, &r, ePBC, box, aps,
r_distance, r_scale, r_shell,
oenv, opt2fn_null("-ip", NFILE, fnm), deltaR, enum_rot,
bCheckAllPairDist);
{ "-renumber", FALSE, etBOOL, {&bRenum}, "Renumber residues" }
};
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
if (bRandom && (seed == 0))
{
t_atoms *atoms,
real rmin, int *seed)
{
- int i, ei,nw;
+ int i, ei, nw;
real rmin2;
rvec dx;
gmx_large_int_t maxrand;
"If you specify a salt concentration existing ions are not taken into "
"account. In effect you therefore specify the amount of salt to be added.",
};
- static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
- static const char *p_name = "NA", *n_name = "CL";
- static real rmin = 0.6, conc = 0;
- static int seed = 1993;
+ static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
+ static const char *p_name = "NA", *n_name = "CL";
+ static real rmin = 0.6, conc = 0;
+ static int seed = 1993;
static gmx_bool bNeutral = FALSE;
- static t_pargs pa[] = {
+ static t_pargs pa[] = {
{ "-np", FALSE, etINT, {&p_num}, "Number of positive ions" },
{ "-pname", FALSE, etSTR, {&p_name}, "Name of the positive ion" },
{ "-pq", FALSE, etINT, {&p_q}, "Charge of the positive ion" },
"Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [TT].tpr[tt] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
{ "-neutral", FALSE, etBOOL, {&bNeutral}, "This option will add enough ions to neutralize the system. These ions are added on top of those specified with [TT]-np[tt]/[TT]-nn[tt] or [TT]-conc[tt]. "}
};
- t_topology top;
+ t_topology top;
rvec *x, *v;
real vol, qtot;
matrix box;
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
/* Check input for something sensible */
if ((p_num < 0) || (n_num < 0))
}
iqtot = gmx_nint(qtot);
-
+
if (conc > 0)
{
/* Compute number of ions to be added */
- vol = det(box);
+ vol = det(box);
nsalt = gmx_nint(conc*vol*AVOGADRO/1e24);
p_num = abs(nsalt*n_q);
n_num = abs(nsalt*p_q);
if ((qdelta % gcd) != 0)
{
gmx_fatal(FARGS, "Can't neutralize this system using -nq %d and"
- " -pq %d.\n", n_q, p_q);
+ " -pq %d.\n", n_q, p_q);
}
-
+
while (qdelta != 0)
{
while (qdelta < 0)
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bFreeze = opt2bSet("-of", NFILE, fnm) || opt2parg_bSet("-freeze", asize(pa), pa);
bDisre = bDisre || opt2parg_bSet("-disre_dist", npargs, pa);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bACF = opt2bSet("-acf", NFILE, fnm);
if (bACF && nmol != 1)
{
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
- fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
+ fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
bMicel = opt2bSet("-nm", NFILE, fnm);
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, npargs,
- ppa, asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, npargs,
+ ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
/* NN-loop? If so, what estimator to use ?*/
NN = 1;
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) &&
opt2parg_bSet("-ahxend", asize(pa), pa));
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
int nfspect, nfxpm, nfraw;
output_env_t oenv;
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bFourier = opt2bSet("-Spect", NFILE, fnm);
bRawOut = opt2bSet("-or", NFILE, fnm);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE | PCA_TIME_UNIT,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE | PCA_TIME_UNIT,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
#ifdef HAVE_LIBGSL
please_cite(stdout, "Spoel2006d");
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fp = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
do_enxnms(fp, &nre, &enm);
};
#define NFILE asize(fnm)
edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
- parse_common_args(&argc, argv, 0,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
indexfile = ftp2fn_null(efNDX, NFILE, fnm);
EdiFile = ftp2fn(efEDI, NFILE, fnm);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
- 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
+ 0, NULL, &oenv))
+ {
+ return 0;
+ }
stxfile = ftp2fn_null(efSTX, NFILE, fnm);
if (opt2bSet("-n", NFILE, fnm))
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE, NFILE, fnm,
+ asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fprintf(stderr, "Will truncate at %f nm\n", truncate);
bCalcN = opt2bSet("-no", NFILE, fnm);
char buf[256], buf2[64];
gmx_bool bSucces;
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
data_out = ffopen(opt2fn("-dat", NFILE, fnm), "w");
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
trxfnm = ftp2fn(efTRX, NFILE, fnm);
ndxfnm = ftp2fn_null(efNDX, NFILE, fnm);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
ft = select_ftype(opt[0], &nft, &mult);
gmx_bool bRMS;
output_env_t oenv;
- parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc,
+ 0, NULL, &oenv))
+ {
+ return 0;
+ }
get_stx_coordnum (opt2fn("-f1", NFILE, fnm), &nat1);
get_stx_coordnum (opt2fn("-f2", NFILE, fnm), &nat2);
if (nat1 != nat2)
real dim_factor;
output_env_t oenv;
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
trx_file = ftp2fn_null(efTRX, NFILE, fnm);
tps_file = ftp2fn_null(efTPS, NFILE, fnm);
ndx_file = ftp2fn_null(efNDX, NFILE, fnm);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* Read tpr file for volume and number of harmonic terms */
read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &tpx, TRUE, &version, &generation);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
indexfile = ftp2fn_null(efNDX, NFILE, fnm);
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit,
&xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
};
output_env_t oenv = NULL;
- parse_common_args(&argc, argv, 0,
- 0, NULL, 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, 0,
+ 0, NULL, 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
return 0;
}
const char *sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
output_env_t oenv;
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (nslices < 1)
{
gmx_fatal(FARGS, "Can not have nslices < 1");
/* Estimate the reciprocal space part error of the SPME Ewald sum. */
static real estimate_reciprocal(
- t_inputinfo *info,
- rvec x[], /* array of particles */
- real q[], /* array of charges */
- int nr, /* number of charges = size of the charge array */
+ t_inputinfo *info,
+ rvec x[], /* array of particles */
+ real q[], /* array of charges */
+ int nr, /* number of charges = size of the charge array */
FILE gmx_unused *fp_out,
- gmx_bool bVerbose,
- unsigned int seed, /* The seed for the random number generator */
- int *nsamples, /* Return the number of samples used if Monte Carlo
- * algorithm is used for self energy error estimate */
- t_commrec *cr)
+ gmx_bool bVerbose,
+ unsigned int seed, /* The seed for the random number generator */
+ int *nsamples, /* Return the number of samples used if Monte Carlo
+ * algorithm is used for self energy error estimate */
+ t_commrec *cr)
{
real e_rec = 0; /* reciprocal error estimate */
real e_rec1 = 0; /* Error estimate term 1*/
PCA_Flags = PCA_NOEXIT_ON_ARGS;
PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
- parse_common_args(&argc, argv, PCA_Flags,
- NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_Flags,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc,
+ 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (!bTUNE)
{
char **legp, buf[STRLEN];
gmx_rmpbc_t gpbc = NULL;
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
snew(top, 1);
ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm),
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
+ &oenv))
+ {
+ return 0;
+ }
/* Calculate axis */
axis = toupper(axtitle[0]) - 'X';
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
axis1 = ffopen(opt2fn("-a1", NFILE, fnm), "w");
axis2 = ffopen(opt2fn("-a2", NFILE, fnm), "w");
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, 0, NULL, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, 0, NULL, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
snew(xr, 1);
{ efXVG, "-hq", "hq", ffOPTWR },
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (bCM || closet[0][0] != 'n' || rdft[0][0] == 'm' || rdft[0][6] == 'm')
{
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW
- | PCA_BE_NICE, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW
+ | PCA_BE_NICE, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
+ &oenv))
+ {
+ return 0;
+ }
/* parse enumerated options: */
ewhat = nenum(what);
if (ewhat == ewRho || ewhat == ewRhoSc)
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bRMS = opt2bSet("-rms", NFILE, fnm);
bScale = opt2bSet("-scl", NFILE, fnm);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
+ &oenv))
+ {
+ return 0;
+ }
bReadPDB = ftp2bSet(efPDB, NFILE, fnm);
devfn = opt2fn_null("-od", NFILE, fnm);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x_ref, NULL, box, bMW);
matrix box;
output_env_t oenv;
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
cg = mk_charge(&top->atoms, &(top->cgs), &ncg);
nthreads = gmx_omp_get_max_threads();
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* check that binwidth not smaller than smallers distance */
check_binwidth(binwidth);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (solsize < 0)
{
solsize = 1e-3;
{ efXVG, "-sq", "sq", ffWRITE },
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fnTPS = ftp2fn(efTPS, NFILE, fnm);
fnTRX = ftp2fn(efTRX, NFILE, fnm);
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
int npargs;
npargs = asize(pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
val = read_xvg_time(opt2fn("-f", NFILE, fnm), bHaveT,
opt2parg_bSet("-b", npargs, pa), tb-ttol,
int cur = 0;
#define next (1-cur)
- parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc),
- desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc),
+ desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bBham = (opt2parg_bSet("-A", asize(pa), pa) ||
opt2parg_bSet("-B", asize(pa), pa) ||
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
two_pi = 2/M_PI;
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
sfree(xtop);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
snew(top, 1);
snew(ir, 1);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
TRUE);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (bMol)
{
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
+ asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bIndex = ftp2bSet(efNDX, NFILE, fnm);
bDeMux = ftp2bSet(efXVG, NFILE, fnm);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
- PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc,
- 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
+ PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc,
+ 0, NULL, &oenv))
+ {
+ return 0;
+ }
top_file = ftp2fn(efTPS, NFILE, fnm);
init_top(&top);
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
sfree(x);
seconds = gettime();
- parse_common_args(&argc, argv, PCA_NOEXIT_ON_ARGS,
- NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_NOEXIT_ON_ARGS,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc,
+ 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* Store the remaining unparsed command line entries in a string which
* is then attached to the mdrun command line */
FILE *fp;
t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
matfile = opt2fn_null("-om", NFILE, fnm);
if (opt2parg_bSet("-fr", NPA, pa))
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (bMol || bMass)
{
opt.stepchange = 100;
opt.stepUpdateContrib = 100;
- parse_common_args(&argc, argv, PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &opt.oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &opt.oenv))
+ {
+ return 0;
+ }
opt.unit = nenum(en_unit);
opt.bsMethod = nenum(en_bsMethod);
int i, nres;
char **resnm;
- parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
for (i = 1; (i < argc); i++)
{
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, NPA, pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
+ NFILE, fnm, NPA, pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
etitle = nenum(title);
elegend = nenum(legend);
}
-void parse_common_args(int *argc, char *argv[], unsigned long Flags,
- int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
- int ndesc, const char **desc,
- int nbugs, const char **bugs,
- output_env_t *oenv)
+gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
+ int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
+ int ndesc, const char **desc,
+ int nbugs, const char **bugs,
+ output_env_t *oenv)
{
gmx_bool bHelp = FALSE, bHidden = FALSE, bVerbose = FALSE;
const char *manstr[] = {
gmx_cmd(argv[1]);
}
}
- if (bExit)
- {
- gmx_finalize_par();
-
- exit(0);
- }
+ return !bExit;
#undef FF
}
* array must be terminated by a NULL pointer
*/
-void parse_common_args(int *argc, char *argv[], unsigned long Flags,
- int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
- int ndesc, const char **desc,
- int nbugs, const char **bugs,
- output_env_t *oenv);
+gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
+ int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
+ int ndesc, const char **desc,
+ int nbugs, const char **bugs,
+ output_env_t *oenv);
/* Get arguments from the arg-list. The arguments extracted
* are removed from the list. If manual is NULL a default message is displayed
* when errors are encountered. The Flags argument, when non-0 enables
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
- 0, NULL, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
+ 0, NULL, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if ((x11 = GetX11(&argc, argv)) == NULL)
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
- 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
+ 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
if ((x11 = GetX11(&argc, argv)) == NULL)
{
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME,
- NFILE, fnm, 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
+ NFILE, fnm, 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
infile = opt2fn("-s", NFILE, fnm);
read_tps_conf(infile, title, &top, &ePBC, &x, NULL, box, FALSE);
"Dihedral angle force constant (kJ/mol/rad^2)" }
};
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
bRTP = opt2bSet("-r", NFILE, fnm);
bTOP = opt2bSet("-o", NFILE, fnm);
/* C89 requirements mean that these struct members cannot be used in
"Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure." }
};
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fn1 = opt2fn_null("-f", NFILE, fnm);
fn2 = opt2fn_null("-f2", NFILE, fnm);
{ "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" }
};
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
+ {
+ return 0;
+ }
if (ftp2bSet(efTPX, NFILE, fnm))
init_ir(ir, opts);
/* Parse the command line */
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
wi = init_warning(TRUE, maxwarn);
};
#define NPARGS asize(pa)
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
+ 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* Force field selection, interactive or direct */
choose_ff(strcmp(ff, "select") == 0 ? NULL : ff,
int nerror = 0;
/* Parse the command line */
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* Convert int to gmx_large_int_t */
nsteps_req = nsteps_req_int;
#define NFILE asize(fnm)
/* Command line options ! */
- gmx_bool bPartDec = FALSE;
- gmx_bool bDDBondCheck = TRUE;
- gmx_bool bDDBondComm = TRUE;
- gmx_bool bTunePME = TRUE;
- gmx_bool bTestVerlet = FALSE;
- gmx_bool bVerbose = FALSE;
- gmx_bool bCompact = TRUE;
- gmx_bool bSepPot = FALSE;
- gmx_bool bRerunVSite = FALSE;
- gmx_bool bIonize = FALSE;
- gmx_bool bConfout = TRUE;
- gmx_bool bReproducible = FALSE;
-
- int npme = -1;
- int nmultisim = 0;
- int nstglobalcomm = -1;
- int repl_ex_nst = 0;
- int repl_ex_seed = -1;
- int repl_ex_nex = 0;
- int nstepout = 100;
- int resetstep = -1;
- gmx_large_int_t nsteps = -2; /* the value -2 means that the mdp option will be used */
-
- rvec realddxyz = {0, 0, 0};
- const char *ddno_opt[ddnoNR+1] =
+ gmx_bool bPartDec = FALSE;
+ gmx_bool bDDBondCheck = TRUE;
+ gmx_bool bDDBondComm = TRUE;
+ gmx_bool bTunePME = TRUE;
+ gmx_bool bTestVerlet = FALSE;
+ gmx_bool bVerbose = FALSE;
+ gmx_bool bCompact = TRUE;
+ gmx_bool bSepPot = FALSE;
+ gmx_bool bRerunVSite = FALSE;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bConfout = TRUE;
+ gmx_bool bReproducible = FALSE;
+
+ int npme = -1;
+ int nmultisim = 0;
+ int nstglobalcomm = -1;
+ int repl_ex_nst = 0;
+ int repl_ex_seed = -1;
+ int repl_ex_nex = 0;
+ int nstepout = 100;
+ int resetstep = -1;
+ gmx_large_int_t nsteps = -2; /* the value -2 means that the mdp option will be used */
+
+ rvec realddxyz = {0, 0, 0};
+ const char *ddno_opt[ddnoNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
- const char *dddlb_opt[] =
+ const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
- const char *thread_aff_opt[threadaffNR+1] =
+ const char *thread_aff_opt[threadaffNR+1] =
{ NULL, "auto", "on", "off", NULL };
- const char *nbpu_opt[] =
+ const char *nbpu_opt[] =
{ NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
- real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
- char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
- real cpt_period = 15.0, max_hours = -1;
- gmx_bool bAppendFiles = TRUE;
- gmx_bool bKeepAndNumCPT = FALSE;
- gmx_bool bResetCountersHalfWay = FALSE;
- output_env_t oenv = NULL;
- const char *deviceOptions = "";
+ real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
+ char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
+ real cpt_period = 15.0, max_hours = -1;
+ gmx_bool bAppendFiles = TRUE;
+ gmx_bool bKeepAndNumCPT = FALSE;
+ gmx_bool bResetCountersHalfWay = FALSE;
+ output_env_t oenv = NULL;
+ const char *deviceOptions = "";
- gmx_hw_opt_t hw_opt = {0, 0, 0, 0, threadaffSEL, 0, 0, NULL};
+ gmx_hw_opt_t hw_opt = {0, 0, 0, 0, threadaffSEL, 0, 0, NULL};
- t_pargs pa[] = {
+ t_pargs pa[] = {
{ "-pd", FALSE, etBOOL, {&bPartDec},
"Use particle decompostion" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
- unsigned long Flags, PCA_Flags;
- ivec ddxyz;
- int dd_node_order;
- gmx_bool bAddPart;
- FILE *fplog, *fpmulti;
- int sim_part, sim_part_fn;
- const char *part_suffix = ".part";
- char suffix[STRLEN];
- int rc;
- char **multidir = NULL;
+ unsigned long Flags, PCA_Flags;
+ ivec ddxyz;
+ int dd_node_order;
+ gmx_bool bAddPart;
+ FILE *fplog, *fpmulti;
+ int sim_part, sim_part_fn;
+ const char *part_suffix = ".part";
+ char suffix[STRLEN];
+ int rc;
+ char **multidir = NULL;
cr = init_par();
}
*/
- parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
/* we set these early because they might be used in init_multisystem()
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff