int gmx_genion(int argc, char *argv[])
{
const char *desc[] = {
"[TT]genion[tt] replaces solvent molecules by monoatomic ions at",
"the position of the first atoms with the most favorable electrostatic",
"potential or at random. The potential is calculated on all atoms, using",
"normal GROMACS particle-based methods (in contrast to other methods",
"based on solving the Poisson-Boltzmann equation).",
"The potential is recalculated after every ion insertion.",
"If specified in the run input file, a reaction field, shift function",
"or user function can be used. For the user function a table file",
"can be specified with the option [TT]-table[tt].",
"The group of solvent molecules should be continuous and all molecules",
"should have the same number of atoms.",
"The user should add the ion molecules to the topology file or use",
"the [TT]-p[tt] option to automatically modify the topology.[PAR]",
"The ion molecule type, residue and atom names in all force fields",
"are the capitalized element names without sign. This molecule name",
"should be given with [TT]-pname[tt] or [TT]-nname[tt], and the",
"[TT][molecules][tt] section of your topology updated accordingly,",
"either by hand or with [TT]-p[tt]. Do not use an atom name instead!",
"[PAR]Ions which can have multiple charge states get the multiplicity",
"added, without sign, for the uncommon states only.[PAR]",
"With the option [TT]-pot[tt] the potential can be written as B-factors",
"in a [TT].pdb[tt] file (for visualisation using e.g. Rasmol).",
"The unit of the potential is 1000 kJ/(mol e), the scaling be changed",
"with the [TT]-scale[tt] option.[PAR]",
"For larger ions, e.g. sulfate we recommended using [TT]genbox[tt]."
};
const char *bugs[] = {
"Calculation of the potential is not reliable, therefore the [TT]-random[tt] option is now turned on by default.",
"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, scale = 0.001, conc = 0;
static int seed = 1993;
static gmx_bool bRandom = TRUE, bNeutral = FALSE;
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" },
{ "-nn", FALSE, etINT, {&n_num}, "Number of negative ions" },
{ "-nname", FALSE, etSTR, {&n_name}, "Name of the negative ion" },
{ "-nq", FALSE, etINT, {&n_q}, "Charge of the negative ion" },
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance between ions" },
{ "-random", FALSE, etBOOL, {&bRandom}, "Use random placement of ions instead of based on potential. The rmin option should still work" },
{ "-seed", FALSE, etINT, {&seed}, "Seed for random number generator" },
{ "-scale", FALSE, etREAL, {&scale}, "Scaling factor for the potential for [TT]-pot[tt]" },
{ "-conc", FALSE, etREAL, {&conc},
"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]. "}
};
gmx_mtop_t *mtop;
gmx_localtop_t *top;
t_inputrec inputrec;
t_commrec *cr;
t_mdatoms *mdatoms;
gmx_enerdata_t enerd;
t_graph *graph;
t_forcerec *fr;
rvec *x, *v;
real *pot, vol, qtot;
matrix box;
t_atoms atoms;
t_pbc pbc;
int *repl;
atom_id *index;
char *grpname;
gmx_bool *bSet, bPDB;
int i, nw, nwa, nsa, nsalt, iqtot;
FILE *fplog;
output_env_t oenv;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efXVG, "-table", "table", ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTO, "-o", NULL, ffWRITE },
{ efLOG, "-g", "genion", ffWRITE },
{ efPDB, "-pot", "pot", ffOPTWR },
{ efTOP, "-p", "topol", ffOPTRW }
};
#define NFILE asize(fnm)
parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bPDB = ftp2bSet(efPDB, NFILE, fnm);
if (bRandom && bPDB)
{
fprintf(stderr, "Not computing potential with random option!\n");
bPDB = FALSE;
}
/* Check input for something sensible */
if ((p_num < 0) || (n_num < 0))
{
gmx_fatal(FARGS, "Negative number of ions to add?");
}
snew(mtop, 1);
snew(top, 1);
fplog = init_calcpot(ftp2fn(efLOG, NFILE, fnm), ftp2fn(efTPX, NFILE, fnm),
opt2fn("-table", NFILE, fnm), mtop, top, &inputrec, &cr,
&graph, &mdatoms, &fr, &enerd, &pot, box, &x, oenv);
atoms = gmx_mtop_global_atoms(mtop);
qtot = 0;
for (i = 0; (i < atoms.nr); i++)
{
qtot += atoms.atom[i].q;
}
iqtot = gmx_nint(qtot);
if (conc > 0)
{
/* Compute number of ions to be added */
vol = det(box);
nsalt = gmx_nint(conc*vol*AVOGADRO/1e24);
p_num = abs(nsalt*n_q);
n_num = abs(nsalt*p_q);
}
if (bNeutral)
{
int qdelta = p_num*p_q + n_num*n_q + iqtot;
/* Check if the system is neutralizable
* is (qdelta == p_q*p_num + n_q*n_num) solvable for p_num and n_num? */
int gcd = greatest_common_divisor(n_q, 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);
}
while (qdelta != 0)
{
while (qdelta < 0)
{
p_num++;
qdelta += p_q;
}
while (qdelta > 0)
{
n_num++;
qdelta += n_q;
}
}
}
if ((p_num == 0) && (n_num == 0))
{
if (!bPDB)
{
fprintf(stderr, "No ions to add and no potential to calculate.\n");
exit(0);
}
nw = 0;
nsa = 0; /* to keep gcc happy */
}
else
{
printf("Will try to add %d %s ions and %d %s ions.\n",
p_num, p_name, n_num, n_name);
printf("Select a continuous group of solvent molecules\n");
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nwa, &index, &grpname);
for (i = 1; i < nwa; i++)
{
if (index[i] != index[i-1]+1)
{
gmx_fatal(FARGS, "The solvent group %s is not continuous: "
"index[%d]=%d, index[%d]=%d",
grpname, i, index[i-1]+1, i+1, index[i]+1);
}
}
nsa = 1;
while ((nsa < nwa) &&
(atoms.atom[index[nsa]].resind ==
atoms.atom[index[nsa-1]].resind))
{
nsa++;
}
if (nwa % nsa)
{
gmx_fatal(FARGS, "Your solvent group size (%d) is not a multiple of %d",
nwa, nsa);
}
nw = nwa/nsa;
fprintf(stderr, "Number of (%d-atomic) solvent molecules: %d\n", nsa, nw);
if (p_num+n_num > nw)
{
gmx_fatal(FARGS, "Not enough solvent for adding ions");
}
}
if (opt2bSet("-p", NFILE, fnm))
{
update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
}
snew(bSet, nw);
snew(repl, nw);
snew(v, atoms.nr);
snew(atoms.pdbinfo, atoms.nr);
set_pbc(&pbc, inputrec.ePBC, box);
/* Now loop over the ions that have to be placed */
do
{
if (!bRandom)
{
calc_pot(fplog, cr, mtop, &inputrec, top, x, fr, &enerd, mdatoms, pot, box, graph);
if (bPDB || debug)
{
char buf[STRLEN];
if (debug)
{
sprintf(buf, "%d_%s", p_num+n_num, ftp2fn(efPDB, NFILE, fnm));
}
else
{
strcpy(buf, ftp2fn(efPDB, NFILE, fnm));
}
for (i = 0; (i < atoms.nr); i++)
{
atoms.pdbinfo[i].bfac = pot[i]*scale;
}
write_sto_conf(buf, "Potential calculated by genion",
&atoms, x, v, inputrec.ePBC, box);
bPDB = FALSE;
}
}
if ((p_num > 0) && (p_num >= n_num))
{
insert_ion(nsa, &nw, bSet, repl, index, pot, x, &pbc,
1, p_q, p_name, mdatoms, rmin, bRandom, &seed);
p_num--;
}
else if (n_num > 0)
{
insert_ion(nsa, &nw, bSet, repl, index, pot, x, &pbc,
-1, n_q, n_name, mdatoms, rmin, bRandom, &seed);
n_num--;
}
}
while (p_num+n_num > 0);
fprintf(stderr, "\n");
if (nw)
{
sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
}
sfree(atoms.pdbinfo);
atoms.pdbinfo = NULL;
write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *mtop->name, &atoms, x, NULL,
inputrec.ePBC, box);
thanx(stderr);
gmx_log_close(fplog);
return 0;
}
int main(int argc, char **argv)
{
FILE *input;
int num_lineas;
int h,i,j,k,l;
int var;
int index;
float El_mayor;
/*---------------------------------------------------------
Verifica cuales archivos fueron usados como input y se asegura de que solo haya cargado uno.
-----------------------------------------------------------*/
printf("Este programa se ejecutó con %d argumento(s):\n",argc-1);
for(i=1;i<argc;i++){
printf("%s\n", argv[i]);
}
if(argc!=2){
printf("se necesita solo un argumento además del nombre del ejecutable!\n EXIT!\n");
exit(1);
}
else{
printf("El archivo a usar es %s\n", argv[1]);
}
//--------------------------------------------------------
input=fopen(argv[1],"r");
if(!input){
printf("surgió un problema abriendo el archivo\n");
exit(1);
}
/*---------------------------------------------------------
toma como archivo base el primer argumento y cuenta sus lineas
-----------------------------------------------------------*/
num_lineas=0;
while ((var = fgetc(input)) != EOF){
if (var =='\n')
++num_lineas;
}
printf("Número de lineas del archivo:\n -->%d\n",num_lineas);
/*---------------------------------------------------------
Data allocation
-----------------------------------------------------------*/
float *x_axis;
float *y_axis;
float *z_axis;
x_axis = malloc(num_lineas * sizeof(float));
y_axis = malloc(num_lineas * sizeof(float));
z_axis = malloc(num_lineas * sizeof(float));
/* if(!x_axis||!y_axis||!z_axis){
printf("Algo salió mal con la reserva de espacio para los arrays x, y o z\n");
exit(1);
}*/
/*---------------------------------------------------------
Registro de Datos en los arrays
-----------------------------------------------------------*/
rewind(input);
for(j=0;j<num_lineas;j++){
fscanf(input, "%f %f %f",&x_axis[j],&y_axis[j],&z_axis[j]);
if(!x_axis[j]||!y_axis[j]||!z_axis[j]){
printf("Existe una linea vacia o hay un problema con la linea %d en el archivo\n",j);
exit(1);
}
}
/*
for(j=0;j<num_lineas;j++){
printf("%f %f %f\n",x_axis[j], y_axis[j], z_axis[j]);
}
*/
//Checkpoint
/*---------------------------------------------------------
Calculo de potencial, filtro
-------------------------------------------------*/
float datum;
float phi[num_lineas];
index =-1;
float a,b,c,d,e,f;
for(k=0;k<num_lineas;k++){
datum=0.0;
phi[k]=0.0;
a=x_axis[k];
b=y_axis[k];
c=z_axis[k];
for(l=0;l<num_lineas;l++){
d=x_axis[l];
e=y_axis[l];
f=z_axis[l];
if (l!=k){
datum+=calc_pot(a,b,c,d,e,f);
}
}
phi[k]=datum;
if(El_mayor<phi[k]){
El_mayor=phi[k];
index=k;
}
/*
if(El_mayor==phi[k]){
printf("Existen dos potenciales iguales\n");
}
*/
}
//--------------------------------------------------------
if(index==-1){
printf("index has not evolved\n");
}
/*---------------------------------------------------------
Entrega de datos
-----------------------------------------------------------*/
printf("---------------------\nLa posicion del minimo de potencial es:\n\n%f %f %f\n\n",x_axis[index], y_axis[index], z_axis[index]);
/*---------------------------------------------------------
FIN
-----------------------------------------------------------*/
fclose(input);
return 0;
}
