static int read_charmm_extrablock(fio_fd fd, int charmm, int reverseEndian,
float *unitcell) {
int i, input_integer[2], rec_scale;
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale = RECSCALE64BIT;
} else {
rec_scale = RECSCALE32BIT;
}
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_EXTRA_BLOCK)) {
/* Leading integer must be 48 */
input_integer[1] = 0;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale)
return DCD_BADREAD;
if (reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) == 48) {
double tmp[6];
if (fio_fread(tmp, 48, 1, fd) != 1) return DCD_BADREAD;
if (reverseEndian)
swap8_aligned(tmp, 6);
for (i=0; i<6; i++) unitcell[i] = (float)tmp[i];
} else {
/* unrecognized block, just skip it */
if (fio_fseek(fd, (input_integer[0]+input_integer[1]), FIO_SEEK_CUR)) return DCD_BADREAD;
}
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
}
return DCD_SUCCESS;
}
static int read_js_timestep(void *v, int natoms, molfile_timestep_t *ts) {
jshandle *js = (jshandle *)v;
int framelen = (natoms * 3 * sizeof(float)) + (6 * sizeof(double));;
/* if we have a valid ts pointer, read the timestep, otherwise skip it */
if (ts != NULL) {
int readlen;
fio_iovec iov[2];
double unitcell[6];
unitcell[0] = unitcell[2] = unitcell[5] = 1.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
/* setup the I/O vector */
iov[0].iov_base = (fio_caddr_t) ts->coords; /* read coordinates */
iov[0].iov_len = natoms * 3 * sizeof(float);
iov[1].iov_base = (fio_caddr_t) &unitcell[0]; /* read PBC unit cell */
iov[1].iov_len = 6 * sizeof(double);
/* Do all of the reads with a single syscall, for peak efficiency. */
/* On smart kernels, readv() causes only one context switch, and */
/* can effeciently scatter the reads to the various buffers. */
readlen = fio_readv(js->fd, &iov[0], 2);
/* check the number of read bytes versus what we expected */
if (readlen != framelen)
return MOLFILE_EOF;
/* perform byte swapping if necessary */
if (js->reverseendian) {
swap4_aligned(ts->coords, natoms * 3);
swap8_aligned(unitcell, 6);
}
/* copy unit cell values into VMD */
ts->A = unitcell[0];
ts->B = unitcell[1];
ts->C = unitcell[2];
ts->alpha = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2;
ts->beta = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2;
ts->gamma = 90.0 - asin(unitcell[5]) * 90.0 / M_PI_2;
} else {
/* skip this frame, seek to the next frame */
if (fio_fseek(js->fd, framelen, FIO_SEEK_CUR))
return MOLFILE_EOF;
}
return MOLFILE_SUCCESS;
}
static void *open_pbeq_read(const char *filepath, const char *filetype,
int *natoms) {
FILE *fd;
pbeq_t *pbeq;
int nclx, ncly, nclz;
int trash, length;
double dcel;
double xbcen, ybcen, zbcen;
double epsw, epsp, conc, tmemb, zmemb, epsm;
int swap=0;
fd = fopen(filepath, "rb");
if (!fd) {
printf("pbeqplugin) Error opening file %s.\n", filepath);
return NULL;
}
// skip first Fortran length record for
// WRITE(UNIT) NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN
if (fread(&length, 4, 1, fd) != 1)
return NULL;
if (fread(&nclx, 4, 1, fd) != 1)
return NULL;
if (fread(&ncly, 4, 1, fd) != 1)
return NULL;
if (fread(&nclz, 4, 1, fd) != 1)
return NULL;
// test endianness first
if (length != 44) {
swap = 1;
swap4_aligned(&length, 1);
if (length != 44) {
printf("pbeqplugin) length record != 44, unrecognized format (length: %d)\n", length);
return NULL;
}
}
if (swap) {
swap4_aligned(&nclx, 1);
swap4_aligned(&ncly, 1);
swap4_aligned(&nclz, 1);
}
// this is a risky strategy for detecting endianness,
// but it works so far, and the charmm potential maps don't
// have version numbers, magic numbers, or anything else that we
// might otherwise use for this purpose.
if ((nclx > 4000 && ncly > 4000 && nclz > 4000) ||
(nclx * ncly * nclz < 0)) {
printf("pbeqplugin) inconclusive byte ordering, bailing out\n");
return NULL;
}
// read the rest of the header
if (fread(&dcel, 8, 1, fd) != 1)
return NULL;
if (fread(&xbcen, 8, 1, fd) != 1)
return NULL;
if (fread(&ybcen, 8, 1, fd) != 1)
return NULL;
if (fread(&zbcen, 8, 1, fd) != 1)
return NULL;
// skip second Fortran length record for
// WRITE(UNIT) NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN
if (fread(&trash, 4, 1, fd) != 1)
return NULL;
// skip first Fortran length record for
// WRITE(UNIT) EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM
if (fread(&trash, 4, 1, fd) != 1)
return NULL;
if (fread(&epsw, 8, 1, fd) != 1)
return NULL;
if (fread(&epsp, 8, 1, fd) != 1)
return NULL;
if (fread(&conc, 8, 1, fd) != 1)
return NULL;
if (fread(&tmemb, 8, 1, fd) != 1)
return NULL;
if (fread(&zmemb, 8, 1, fd) != 1)
return NULL;
if (fread(&epsm, 8, 1, fd) != 1)
return NULL;
// skip second Fortran length record for
// WRITE(UNIT) EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM
if (fread(&trash, 4, 1, fd) != 1)
return NULL;
// byte swap the header data if necessary
if (swap) {
swap8_aligned(&dcel, 1);
swap8_aligned(&xbcen, 1);
swap8_aligned(&ybcen, 1);
swap8_aligned(&zbcen, 1);
swap8_aligned(&epsw, 1);
swap8_aligned(&epsp, 1);
swap8_aligned(&conc, 1);
swap8_aligned(&tmemb, 1);
swap8_aligned(&zmemb, 1);
swap8_aligned(&epsm, 1);
}
#if 0
// print header info for debugging of early versions
printf("pbeqplugin) nclx:%d nxly:%d nclz:%d\n", nclx, ncly, nclz);
printf("pbeqplugin) dcel: %f\n", dcel);
printf("pbeqplugin) x/y/zbcen: %g %g %g\n", xbcen, ybcen, zbcen);
printf("pbeqplugin) epsw/p: %g %g conc: %g tmemb: %g zmemb: %g epsm: %g\n",
epsw, epsp, conc, tmemb, zmemb, epsm);
#endif
/* Allocate and initialize the pbeq structure */
pbeq = new pbeq_t;
pbeq->fd = fd;
pbeq->vol = NULL;
*natoms = MOLFILE_NUMATOMS_NONE;
pbeq->nsets = 1; /* this file contains only one data set */
pbeq->ndata = nclx*ncly*nclz;
pbeq->nclx = nclx;
pbeq->ncly = ncly;
pbeq->nclz = nclz;
pbeq->swap = swap;
pbeq->vol = new molfile_volumetric_t[1];
strcpy(pbeq->vol[0].dataname, "CHARMM PBEQ Potential Map");
pbeq->vol[0].origin[0] = -0.5*((nclx-1) * dcel) + xbcen;
pbeq->vol[0].origin[1] = -0.5*((ncly-1) * dcel) + ybcen;
pbeq->vol[0].origin[2] = -0.5*((nclz-1) * dcel) + zbcen;
// print origin info, for debuggin of early versions
printf("pbeqplugin) box LL origin: %g %g %g\n",
pbeq->vol[0].origin[0],
pbeq->vol[0].origin[1],
pbeq->vol[0].origin[2]);
pbeq->vol[0].xaxis[0] = (nclx-1) * dcel;
pbeq->vol[0].xaxis[1] = 0;
pbeq->vol[0].xaxis[2] = 0;
pbeq->vol[0].yaxis[0] = 0;
pbeq->vol[0].yaxis[1] = (ncly-1) * dcel;
pbeq->vol[0].yaxis[2] = 0;
pbeq->vol[0].zaxis[0] = 0;
pbeq->vol[0].zaxis[1] = 0;
pbeq->vol[0].zaxis[2] = (nclz-1) * dcel;
pbeq->vol[0].xsize = nclx;
pbeq->vol[0].ysize = ncly;
pbeq->vol[0].zsize = nclz;
pbeq->vol[0].has_color = 0;
return pbeq;
}
