int
main (void)
{
extern int Using_Main; /* is main routine being called? */
extern char *Graph_File_Name; /* name of graph input file */
extern char *Geometry_File_Name; /* name of coordinate input file */
extern char *Assign_In_File_Name; /* name of assignment input input file */
extern char *PARAMS_FILENAME; /* name of file with parameter updates */
extern double EIGEN_TOLERANCE; /* tolerance for eigen calculations */
extern int OUTPUT_ASSIGN; /* whether to write assignment to file */
extern int DEBUG_MEMORY; /* debug memory allocation and freeing? */
extern int DEBUG_TRACE; /* trace main execution path */
extern int DEBUG_PARAMS; /* debug flag for reading parameters */
extern long RANDOM_SEED; /* seed for random number generators */
extern int ECHO; /* controls amount of output */
extern int PROMPT; /* prompt for input or not? */
extern int PRINT_HEADERS; /* print lines for output sections? */
extern int MATCH_TYPE; /* matching routine to call */
extern double input_time; /* times data file input */
extern double start_time; /* time partitioning starts */
FILE *fin; /* input file */
FILE *fingeom; /* geometry input file (for inertial method) */
FILE *finassign; /* assignment file if reading in */
FILE *params_file; /* file with parameter value updates */
double *goal; /* desired set sizes */
float *x, *y, *z; /* coordinates for inertial method */
int *start; /* start of edge list for each vertex */
int *adjacency; /* edge list data */
float *ewgts; /* weights for all edges */
int *vwgts; /* weights for all vertices */
int global_method; /* global partitioning method */
int local_method; /* local partitioning method */
int *assignment; /* set number of each vtx (length nvtxs+1) */
double eigtol; /* tolerance in eigenvector calculation */
int nvtxs; /* number of vertices in graph */
int ndims; /* dimension of recursive partitioning */
int architecture; /* 0 => hypercube, d => d-dimensional mesh */
int ndims_tot; /* total number of cube dimensions to divide */
int mesh_dims[3]; /* dimensions of mesh of processors */
long seed; /* for random graph mutations */
int rqi_flag; /* use RQI/Symmlq eigensolver? */
int vmax; /* if so, how many vertices to coarsen down to? */
int igeom; /* geometry dimension if inertial method */
char graphname[NAME_LENGTH]; /* name of graph input file */
char geomname[NAME_LENGTH]; /* name of geometry input file */
char inassignname[NAME_LENGTH]; /* assignment input file name */
char outassignname[NAME_LENGTH]; /* assignment output file name */
char outfilename[NAME_LENGTH]; /* name of output file */
char *outassignptr; /* name or null pointer for output assignment */
char *outfileptr; /* name or null pointer for output file */
int another; /* run another problem? */
double time; /* timing marker */
int flag; /* return code from input routines */
double seconds(); /* returns elapsed time in seconds */
int affirm();
int input_graph(), input_geom();
void input_queries(), read_params(), clear_timing();
/*malloc_debug(2);*/
if (DEBUG_TRACE > 0) {
printf("<Entering main>\n");
}
if (PRINT_HEADERS) {
printf("\n Chaco 2.0\n");
printf(" Sandia National Laboratories\n\n");
}
Using_Main = TRUE;
another = TRUE;
params_file = fopen(PARAMS_FILENAME, "r");
if (params_file == NULL && DEBUG_PARAMS > 1) {
printf("Parameter file `%s' not found; using default parameters.\n",
PARAMS_FILENAME);
}
while (another) {
start_time = time = seconds();
x = y = z = NULL;
goal = NULL;
assignment = NULL;
read_params(params_file);
input_queries(&fin, &fingeom, &finassign, graphname, geomname, inassignname,
outassignname, outfilename,
&architecture, &ndims_tot, mesh_dims,
&global_method, &local_method, &rqi_flag, &vmax, &ndims);
if (global_method == 7)
Assign_In_File_Name = inassignname;
else
Assign_In_File_Name = NULL;
if (OUTPUT_ASSIGN > 0)
outassignptr = outassignname;
else
outassignptr = NULL;
if (ECHO < 0)
outfileptr = outfilename;
else
outfileptr = NULL;
flag = input_graph(fin, graphname, &start, &adjacency, &nvtxs, &vwgts, &ewgts);
if (flag) {
sfree(ewgts);
sfree(vwgts);
sfree(adjacency);
sfree(start);
goto skip;
}
Graph_File_Name = graphname;
assignment = smalloc(nvtxs * sizeof(int));
if (global_method == 7) {
flag = input_assign(finassign, inassignname, nvtxs, assignment);
if (flag)
goto skip;
Assign_In_File_Name = inassignname;
}
if (global_method == 3 ||
(MATCH_TYPE == 5 && (global_method == 1 ||
(global_method == 2 && rqi_flag)))) {
/* Read in geometry data. */
flag = input_geom(fingeom, geomname, nvtxs, &igeom, &x, &y, &z);
if (flag)
goto skip;
Geometry_File_Name = geomname;
}
else {
x = y = z = NULL;
}
input_time += seconds() - time;
eigtol = EIGEN_TOLERANCE;
seed = RANDOM_SEED;
interface(nvtxs, start, adjacency, vwgts, ewgts, x, y, z,
outassignptr, outfileptr,
assignment,
architecture, ndims_tot, mesh_dims, goal,
global_method, local_method, rqi_flag, vmax, ndims,
eigtol, seed);
skip:
if (global_method == 3) {
if (z != NULL)
sfree(z);
if (y != NULL)
sfree(y);
if (x != NULL)
sfree(x);
}
sfree(assignment);
if (DEBUG_MEMORY > 0) {
printf("\n");
}
if (PROMPT) {
another = affirm("\nRun Another Problem");
}
else {
another = affirm("");
}
if (another) {
clear_timing();
printf("\n------------------------------------------------\n\n");
fflush(stdout);
}
}
if (params_file != NULL)
fclose(params_file);
if (DEBUG_TRACE > 1) {
printf("<Leaving main>\n");
}
return(0);
}
int main (int argc, char *argv[]) {
static char usage[] = {
"Calculate positions of pseudo-atoms in a model for a transmembrane channel and\n"
"write output to FILE or pore.pdb and pore.itp.\n\n"
" -h\t\t show help\n"
" -v\t\t be verbose (= -debuglevel 30 )\n"
" -debug <NUM>\t set debuglevel (0..100)\n"
" -spec <NUM>\t default species id\n"
" -showspec\t show hard coded species\n\n"
" -o FILE\t pdb coordinate file\n"
" -s FILE\t itp topology file\n"
"\n"
" -f <file>\t read pore description from file (see below)\n"
" -R <r>\t Outer radius of the model\n"
" -P <r> <l>\t Pore region: inner radius and length\n"
" -M <r> <l>\t Mouth region: largest inner radius and length\n"
" -b dmin dmax g_min g_max (repeatable)\n"
"\t\tform bonds with angle gamma when atoms are no further apart\n"
"\t\tthan dmax Ang and g_min <= gamma <= g_max, g from [0°..90°] )\n"
" -c\t\t only write connectivity to output, no bond length or kB, kA\n"
" -x\t\t neither connectivity nor bond length to output (isolated atoms)\n"
" -kB <c>\t Force constant of bonds, in kJ mol^-1 nm^-2\n"
" -kA <c>\t Force constant of angles, in kJ mol^-1 rad^-2\n"
" -cc\t\t Center ccordinates on cavitybox, not on unitcell\n"
"\n"
"Pore volume calculation (setting any of these switches on profile calculation):\n"
"In order to enable volume calculation, set -volume explicitly!\n"
"ATTENTION: all these LENGTHs are in NANO METRE not Angstrom !\n"
" -profile [<file>] calculate the profile in addition to the volume\n"
" -z1, -z2 <z> profile between z1 and z2\n"
" -Rmax <r> integrate out to Rmax (also use for the total volume\n"
" integration if -profile is set)\n"
" -npoints <N> number of points per dimension in the integrals\n"
" -T temp Temperature in Kelvin [300]\n"
" -wca If set, only use the repulsive part of the Lennard-Jones\n"
" potential (split after Weeks, Chandler & Andersen [1971])\n"
" -plot xfarbe output of the potential in z slices\n"
" -nzplot number of plot slices \n"
"\nDescription of the input file:\n"
"------------------------------\n"
"Instead of using -R (RADIUS), -M (MOUTH), and -P (PORE) one can describe the system\n"
"in a more flexible manner with a geometry in put file. It can contain up to "
"MAXDOMAINS domains (i.e. MOUTH and PORE lines). Allowed lines:\n"
"# comment (skipped)\n"
"# RADIUS is the global outer radius (in Angstrom) of the cylinder\n"
"RADIUS r_outer\n"
"# domain type and radius at the upper and lower end of the domain;\n"
"# r_lower of domain i and r_upper of domain i+1 are typically identical\n"
"MOUTH r_upper r_lower length [species]\n"
"PORE r_upper r_lower length [species]\n"
};
int i, n_atoms, n_bonds, n_angles, n_bc;
int error;
real vol;
FILE *fp;
/*
segmentation fault if arrays to large
--->>
now that I have learned to calloc I should rewrite this
on purely aesthetical grounds !
<<----
*/
struct pdb_ATOM model[TOTALSITES];
struct itp_bond bonds[MAXBONDS];
struct itp_angle angles[MAXANGLES];
struct geom geometry;
struct std_input in;
struct potpars potential = {
NULL,
TEMPERATURE,
NFREEDOM_SPC,
CSIX_OW_MTH, CTWELVE_OW_MTH, 0.0,
0, NULL, NULL,
N_GAUSSLEG
};
struct pprofile profile = {
"LJprofile.dat",
FALSE,
FALSE,
POT_PLOT_SLICES,
NULL,
NZPROF,
1.5,
-2,2,
NULL
};
/* argument processing */
/* *** no sanity checks *** */
n_atoms = 0; /* number of sites ('atoms') in the model */
n_bonds = 0; /* number of bonds */
n_angles = 0; /* number of angles between bonds */
n_bc = 0; /* number of constraint conditions for generating bonds */
if (argc < 2) {
printf("Running with default values.\n\nType %s -h for help.\n", argv[0]);
debuglevel = IMPORTANT;
};
/* initialize defaults */
in = default_input ();
potential.u1 = vljcyl; /* use the full Lennard-Jones potential in
the configurational volume calculations
by default */
profile.pp = &potential;
/* rudimentary opt-processing.. yarch */
for (i = 1; i < argc; i++)
{
if (!strcmp(argv[i], "-debug")) {
debuglevel = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-v")) {
debuglevel = VERBOSE;
} else if (!strcmp(argv[i], "-h")) {
print_usage(argv[0],usage);
exit(1);
} else if (!strcmp(argv[i], "-showspec")) {
print_species ();
exit(1);
} else if (!strcmp(argv[i], "-o")) {
in.coordfile = argv[++i];
} else if (!strcmp(argv[i], "-s")) {
in.topofile = argv[++i];
} else if (!strcmp(argv[i], "-f")) {
in.datafile = argv[++i];
} else if (!strcmp(argv[i], "-R")) {
in.r_outer = atof(argv[++i]);
} else if (!strcmp(argv[i], "-M")) {
in.r_mouth = atof(argv[++i]);
in.l_mouth = atof(argv[++i]);
} else if (!strcmp(argv[i], "-P")) {
in.r_pore = atof(argv[++i]);
in.l_pore = atof(argv[++i]);
} else if (!strcmp(argv[i], "-spec")) {
in.specid = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-b")) {
if (n_bc > MAXBONDCONSTRAINTS) {
fatal_error (1,
"Error: too many bond constraints, maximum is %d.\n",
MAXBONDCONSTRAINTS);
}
in.bc[n_bc].serial = n_bc;
in.bc[n_bc].dmin = atof(argv[++i]);
in.bc[n_bc].dmax = atof(argv[++i]);
in.bc[n_bc].gamma_min = atof(argv[++i]);
in.bc[n_bc].gamma_max = atof(argv[++i]);
in.n_bc = ++n_bc;
} else if (!strcmp(argv[i], "-c")) {
in.connectonly = TRUE;
} else if (!strcmp(argv[i], "-x")) {
in.atomsonly = TRUE;
} else if (!strcmp(argv[i], "-cc")) {
in.shiftcbox = TRUE;
} else if (!strcmp(argv[i], "-kB")) {
in.k_bond = atof(argv[++i]);
} else if (!strcmp(argv[i], "-kA")) {
in.k_angle = atof(argv[++i]);
} else if (!strcmp(argv[i], "-volume")) {
profile.bSet = TRUE;
} else if (!strcmp(argv[i], "-z1")) {
profile.bSet = TRUE;
profile.z1 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-z2")) {
profile.bSet = TRUE;
profile.z2 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-Rmax")) {
profile.bSet = TRUE;
profile.Rmax = atof(argv[++i]);
} else if (!strcmp(argv[i], "-profile")) {
profile.bSet = TRUE;
if (i < argc-1 && argv[i+1][0] != '-')
strncpy(profile.fn,argv[++i],STRLEN);
} else if (!strcmp(argv[i], "-npoints")) {
potential.ngaussleg = atof(argv[++i]);
} else if (!strcmp(argv[i], "-T")) {
potential.Temp = atof(argv[++i]);
} else if (!strcmp(argv[i], "-wca")) {
potential.u1 = vRljcyl;
} else if (!strcmp(argv[i], "-plot")) {
profile.bPlot = TRUE;
} else if (!strcmp(argv[i], "-nzplot")) {
profile.bPlot = TRUE;
profile.nzplot = atoi(argv[++i]);
} else {
mesg(OFF,"Unknown option: %s",argv[i]);
};
};
mesg (ALL, "TOTALSITES %d\n", TOTALSITES);
mesg (ALL,
"MAXBONDS %d\nsizeof struct bond %d, sizeof bonds[] %d\n",
MAXBONDS, sizeof (struct itp_bond), sizeof (bonds));
mesg (ALL,
"MAXANGLES %d\nsizeof struct angle %d, sizeof angles[] %d\n",
MAXANGLES, sizeof (struct itp_angle), sizeof (angles));
error = input_geom (&in, &geometry);
setup_domain (&geometry);
unitcell (&geometry);
cavitybox (&geometry);
n_atoms = do_coordinates (model, &geometry);
if (!geometry.atomsonly) {
n_bonds = do_bonds (bonds, model, &geometry);
n_angles = do_angles (angles, bonds, &geometry);
} else {
n_bonds = n_angles = 0;
}
print_geom (&geometry);
mesg (WARN, "\nNumber of sites: %d", n_atoms);
if (!geometry.atomsonly) {
mesg (WARN,
"Number of bonds: %d within max cut-off %5.2f Ang (no double-counting)",
n_bonds, find_dmax (geometry.bc, geometry.nbc));
mesg (WARN, "Number of angles: %d (no double-counting)\n", n_angles);
}
center (model, &geometry);
error = write_topology (model, bonds, angles, &geometry);
error = write_pdb (model, bonds, &geometry);
/*
calculate pore volume, based on J. S. Rowlinson, J Chem Soc,
Faraday Trans. 2, 82 (1986), 1801, (which didnt really work), and
discussion with Andrew Horsefield. */
if (profile.bSet) {
vol = volume(&potential,model,geometry.domain[1],&profile);
/* pore profile (already calculated in volume ) */
fp=fopen(profile.fn,"w");
if (fp) {
for(i=0;i<NZPROF;i++) {
fprintf(fp,"%f %f\n",profile.r[i][0],profile.r[i][1]);
}
fclose(fp);
}
free(profile.r);
}
return error < 0 ? 1 : 0;
};
