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; };