*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/strdb.h"
-typedef struct gmx_structurefactors {
- int nratoms;
- int *p; /* proton number */
- int *n; /* neutron number */
+typedef struct gmx_structurefactors
+{
+ int nratoms;
+ int* p; /* proton number */
+ int* n; /* neutron number */
/* Parameters for the Cromer Mann fit */
- real **a; /* parameter a */
- real **b; /* parameter b */
- real *c; /* parameter c */
- char **atomnm; /* atomname */
+ real** a; /* parameter a */
+ real** b; /* parameter b */
+ real* c; /* parameter c */
+ char** atomnm; /* atomname */
} gmx_structurefactors;
-typedef struct reduced_atom{
+typedef struct reduced_atom
+{
rvec x;
int t;
} reduced_atom;
typedef struct structure_factor
{
- int n_angles;
- int n_groups;
- double lambda;
- double energy;
- double momentum;
- double ref_k;
- double **F;
- int nSteps;
- int total_n_atoms;
+ int n_angles;
+ int n_groups;
+ double lambda;
+ double energy;
+ double momentum;
+ double ref_k;
+ double** F;
+ int nSteps;
+ int total_n_atoms;
} structure_factor;
-extern int * create_indexed_atom_type (reduced_atom_t * atm, int size)
+extern int* create_indexed_atom_type(reduced_atom_t* atm, int size)
{
-/*
- * create an index of the atom types found in a group
- * i.e.: for water index_atp[0]=type_number_of_O and
- * index_atp[1]=type_number_of_H
- *
- * the last element is set to 0
- */
- int *index_atp, i, i_tmp, j;
+ /*
+ * create an index of the atom types found in a group
+ * i.e.: for water index_atp[0]=type_number_of_O and
+ * index_atp[1]=type_number_of_H
+ *
+ * the last element is set to 0
+ */
+ int *index_atp, i, i_tmp, j;
- reduced_atom *att = static_cast<reduced_atom *>(atm);
+ reduced_atom* att = static_cast<reduced_atom*>(atm);
- snew (index_atp, 1);
+ snew(index_atp, 1);
i_tmp = 1;
index_atp[0] = att[0].t;
for (i = 1; i < size; i++)
if (j == i_tmp) /* i.e. no indexed atom type is == to atm[i].t */
{
i_tmp++;
- srenew (index_atp, i_tmp * sizeof (int));
+ srenew(index_atp, i_tmp * sizeof(int));
index_atp[i_tmp - 1] = att[i].t;
}
}
i_tmp++;
- srenew (index_atp, i_tmp * sizeof (int));
+ srenew(index_atp, i_tmp * sizeof(int));
index_atp[i_tmp - 1] = 0;
return index_atp;
}
-
-extern t_complex *** rc_tensor_allocation(int x, int y, int z)
+extern t_complex*** rc_tensor_allocation(int x, int y, int z)
{
- t_complex ***t;
+ t_complex*** t;
int i, j;
snew(t, x);
- snew(t[0], x*y);
- snew(t[0][0], x*y*z);
+ snew(t[0], x * y);
+ snew(t[0][0], x * y * z);
for (j = 1; j < y; j++)
{
- t[0][j] = t[0][j-1] + z;
+ t[0][j] = t[0][j - 1] + z;
}
for (i = 1; i < x; i++)
{
- t[i] = t[i-1] + y;
- t[i][0] = t[i-1][0] + y*z;
+ t[i] = t[i - 1] + y;
+ t[i][0] = t[i - 1][0] + y * z;
for (j = 1; j < y; j++)
{
- t[i][j] = t[i][j-1] + z;
+ t[i][j] = t[i][j - 1] + z;
}
}
return t;
}
-extern void compute_structure_factor (structure_factor_t * sft, matrix box,
- reduced_atom_t * red, int isize, real start_q,
- real end_q, int group, real **sf_table)
+extern void compute_structure_factor(structure_factor_t* sft,
+ matrix box,
+ reduced_atom_t* red,
+ int isize,
+ real start_q,
+ real end_q,
+ int group,
+ real** sf_table)
{
- structure_factor *sf = static_cast<structure_factor *>(sft);
- reduced_atom *redt = static_cast<reduced_atom *>(red);
+ structure_factor* sf = static_cast<structure_factor*>(sft);
+ reduced_atom* redt = static_cast<reduced_atom*>(red);
- t_complex ***tmpSF;
- rvec k_factor;
- real kdotx, asf, kx, ky, kz, krr;
- int kr, maxkx, maxky, maxkz, i, j, k, p, *counter;
+ t_complex*** tmpSF;
+ rvec k_factor;
+ real kdotx, asf, kx, ky, kz, krr;
+ int kr, maxkx, maxky, maxkz, i, j, k, p, *counter;
k_factor[XX] = 2 * M_PI / box[XX][XX];
maxky = gmx::roundToInt(end_q / k_factor[YY]);
maxkz = gmx::roundToInt(end_q / k_factor[ZZ]);
- snew (counter, sf->n_angles);
+ snew(counter, sf->n_angles);
tmpSF = rc_tensor_allocation(maxkx, maxky, maxkz);
-/*
- * The big loop...
- * compute real and imaginary part of the structure factor for every
- * (kx,ky,kz))
- */
+ /*
+ * The big loop...
+ * compute real and imaginary part of the structure factor for every
+ * (kx,ky,kz))
+ */
fprintf(stderr, "\n");
for (i = 0; i < maxkx; i++)
{
- fprintf (stderr, "\rdone %3.1f%% ", (100.0*(i+1))/maxkx);
+ fprintf(stderr, "\rdone %3.1f%% ", (100.0 * (i + 1)) / maxkx);
fflush(stderr);
kx = i * k_factor[XX];
for (j = 0; j < maxky; j++)
if (i != 0 || j != 0 || k != 0)
{
kz = k * k_factor[ZZ];
- krr = std::sqrt (gmx::square(kx) + gmx::square(ky) + gmx::square(kz));
+ krr = std::sqrt(gmx::square(kx) + gmx::square(ky) + gmx::square(kz));
if (krr >= start_q && krr <= end_q)
{
- kr = gmx::roundToInt(krr/sf->ref_k);
+ kr = gmx::roundToInt(krr / sf->ref_k);
if (kr < sf->n_angles)
{
counter[kr]++; /* will be used for the copmutation
{
asf = sf_table[redt[p].t][kr];
- kdotx = kx * redt[p].x[XX] +
- ky * redt[p].x[YY] + kz * redt[p].x[ZZ];
+ kdotx = kx * redt[p].x[XX] + ky * redt[p].x[YY] + kz * redt[p].x[ZZ];
tmpSF[i][j][k].re += std::cos(kdotx) * asf;
tmpSF[i][j][k].im += std::sin(kdotx) * asf;
}
}
}
- } /* end loop on i */
-/*
- * compute the square modulus of the structure factor, averaging on the surface
- * kx*kx + ky*ky + kz*kz = krr*krr
- * note that this is correct only for a (on the macroscopic scale)
- * isotropic system.
- */
+ } /* end loop on i */
+ /*
+ * compute the square modulus of the structure factor, averaging on the surface
+ * kx*kx + ky*ky + kz*kz = krr*krr
+ * note that this is correct only for a (on the macroscopic scale)
+ * isotropic system.
+ */
for (i = 0; i < maxkx; i++)
{
- kx = i * k_factor[XX]; for (j = 0; j < maxky; j++)
+ kx = i * k_factor[XX];
+ for (j = 0; j < maxky; j++)
{
- ky = j * k_factor[YY]; for (k = 0; k < maxkz; k++)
+ ky = j * k_factor[YY];
+ for (k = 0; k < maxkz; k++)
{
- kz = k * k_factor[ZZ]; krr = std::sqrt (gmx::square(kx) + gmx::square(ky)
- + gmx::square(kz)); if (krr >= start_q && krr <= end_q)
+ kz = k * k_factor[ZZ];
+ krr = std::sqrt(gmx::square(kx) + gmx::square(ky) + gmx::square(kz));
+ if (krr >= start_q && krr <= end_q)
{
kr = gmx::roundToInt(krr / sf->ref_k);
if (kr < sf->n_angles && counter[kr] != 0)
{
sf->F[group][kr] +=
- (gmx::square(tmpSF[i][j][k].re) +
- gmx::square(tmpSF[i][j][k].im))/ counter[kr];
+ (gmx::square(tmpSF[i][j][k].re) + gmx::square(tmpSF[i][j][k].im))
+ / counter[kr];
}
}
}
}
-extern gmx_structurefactors_t *gmx_structurefactors_init(const char *datfn)
+extern gmx_structurefactors_t* gmx_structurefactors_init(const char* datfn)
{
/* Read the database for the structure factor of the different atoms */
char line[STRLEN];
- gmx_structurefactors *gsf;
+ gmx_structurefactors* gsf;
double a1, a2, a3, a4, b1, b2, b3, b4, c;
int p;
int i;
int line_no;
char atomn[32];
gmx::FilePtr fp = gmx::openLibraryFile(datfn);
- line_no = 0;
+ line_no = 0;
snew(gsf, 1);
snew(gsf->atomnm, nralloc);
while (get_a_line(fp.get(), line, STRLEN))
{
i = line_no;
- if (sscanf(line, "%s %d %lf %lf %lf %lf %lf %lf %lf %lf %lf",
- atomn, &p, &a1, &a2, &a3, &a4, &b1, &b2, &b3, &b4, &c) == 11)
+ if (sscanf(line, "%s %d %lf %lf %lf %lf %lf %lf %lf %lf %lf", atomn, &p, &a1, &a2, &a3, &a4,
+ &b1, &b2, &b3, &b4, &c)
+ == 11)
{
gsf->atomnm[i] = gmx_strdup(atomn);
gsf->p[i] = p;
}
else
{
- fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n",
- datfn, line_no);
+ fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n", datfn, line_no);
}
}
srenew(gsf->c, gsf->nratoms);
srenew(gsf->p, gsf->nratoms);
- return static_cast<gmx_structurefactors_t *>(gsf);
-
+ return static_cast<gmx_structurefactors_t*>(gsf);
}
-extern void rearrange_atoms (reduced_atom_t * positions, t_trxframe *fr, const int * index,
- int isize, const t_topology * top, gmx_bool flag, gmx_structurefactors_t *gsf)
+extern void rearrange_atoms(reduced_atom_t* positions,
+ t_trxframe* fr,
+ const int* index,
+ int isize,
+ const t_topology* top,
+ gmx_bool flag,
+ gmx_structurefactors_t* gsf)
/* given the group's index, return the (continuous) array of atoms */
{
- int i;
+ int i;
- reduced_atom *pos = static_cast<reduced_atom *>(positions);
+ reduced_atom* pos = static_cast<reduced_atom*>(positions);
if (flag)
{
for (i = 0; i < isize; i++)
{
- pos[i].t =
- return_atom_type (*(top->atoms.atomname[index[i]]), gsf);
+ pos[i].t = return_atom_type(*(top->atoms.atomname[index[i]]), gsf);
}
}
for (i = 0; i < isize; i++)
{
- copy_rvec (fr->x[index[i]], pos[i].x);
+ copy_rvec(fr->x[index[i]], pos[i].x);
}
}
-extern int return_atom_type (const char *name, gmx_structurefactors_t *gsf)
+extern int return_atom_type(const char* name, gmx_structurefactors_t* gsf)
{
- typedef struct {
- const char *name;
+ typedef struct
+ {
+ const char* name;
int nh;
} t_united_h;
- t_united_h uh[] = {
- { "CH1", 1 }, { "CH2", 2 }, { "CH3", 3 },
- { "CS1", 1 }, { "CS2", 2 }, { "CS3", 3 },
- { "CP1", 1 }, { "CP2", 2 }, { "CP3", 3 }
- };
- int i, cnt = 0;
- int *tndx;
- int nrc;
- int fndx = 0;
- int NCMT;
+ t_united_h uh[] = { { "CH1", 1 }, { "CH2", 2 }, { "CH3", 3 }, { "CS1", 1 }, { "CS2", 2 },
+ { "CS3", 3 }, { "CP1", 1 }, { "CP2", 2 }, { "CP3", 3 } };
+ int i, cnt = 0;
+ int* tndx;
+ int nrc;
+ int fndx = 0;
+ int NCMT;
- gmx_structurefactors *gsft = static_cast<gmx_structurefactors *>(gsf);
+ gmx_structurefactors* gsft = static_cast<gmx_structurefactors*>(gsf);
NCMT = gsft->nratoms;
{
if (std::strcmp(name, uh[i].name) == 0)
{
- return NCMT-1+uh[i].nh;
+ return NCMT - 1 + uh[i].nh;
}
}
for (i = 0; (i < NCMT); i++)
{
- if (std::strncmp (name, gsft->atomnm[i], std::strlen(gsft->atomnm[i])) == 0)
+ if (std::strncmp(name, gsft->atomnm[i], std::strlen(gsft->atomnm[i])) == 0)
{
tndx[cnt] = i;
cnt++;
if (cnt == 0)
{
- gmx_fatal(FARGS, "\nError: atom (%s) not in list (%d types checked)!\n",
- name, i);
+ gmx_fatal(FARGS, "\nError: atom (%s) not in list (%d types checked)!\n", name, i);
}
else
{
}
}
-extern int gmx_structurefactors_get_sf(gmx_structurefactors_t *gsf, int elem, real a[4], real b[4], real *c)
+extern int gmx_structurefactors_get_sf(gmx_structurefactors_t* gsf, int elem, real a[4], real b[4], real* c)
{
int success;
int i;
- gmx_structurefactors *gsft = static_cast<gmx_structurefactors *>(gsf);
- success = 0;
+ gmx_structurefactors* gsft = static_cast<gmx_structurefactors*>(gsf);
+ success = 0;
for (i = 0; i < 4; i++)
{
return success;
}
-extern int do_scattering_intensity (const char* fnTPS, const char* fnNDX,
- const char* fnXVG, const char *fnTRX,
- const char* fnDAT,
- real start_q, real end_q,
- real energy, int ng, const gmx_output_env_t *oenv)
+extern int do_scattering_intensity(const char* fnTPS,
+ const char* fnNDX,
+ const char* fnXVG,
+ const char* fnTRX,
+ const char* fnDAT,
+ real start_q,
+ real end_q,
+ real energy,
+ int ng,
+ const gmx_output_env_t* oenv)
{
- int i, *isize, flags = TRX_READ_X, **index_atp;
- t_trxstatus *status;
- char **grpname;
- int **index;
- t_topology top;
- int ePBC;
- t_trxframe fr;
- reduced_atom_t **red;
- structure_factor *sf;
- rvec *xtop;
- real **sf_table;
- matrix box;
- real r_tmp;
-
- gmx_structurefactors_t *gmx_sf;
- real *a, *b, c;
+ int i, *isize, flags = TRX_READ_X, **index_atp;
+ t_trxstatus* status;
+ char** grpname;
+ int** index;
+ t_topology top;
+ int ePBC;
+ t_trxframe fr;
+ reduced_atom_t** red;
+ structure_factor* sf;
+ rvec* xtop;
+ real** sf_table;
+ matrix box;
+ real r_tmp;
+
+ gmx_structurefactors_t* gmx_sf;
+ real * a, *b, c;
snew(a, 4);
snew(b, 4);
gmx_structurefactors_get_sf(gmx_sf, 0, a, b, &c);
- snew (sf, 1);
+ snew(sf, 1);
sf->energy = energy;
/* Read the topology informations */
- read_tps_conf (fnTPS, &top, &ePBC, &xtop, nullptr, box, TRUE);
- sfree (xtop);
+ read_tps_conf(fnTPS, &top, &ePBC, &xtop, nullptr, box, TRUE);
+ sfree(xtop);
/* groups stuff... */
- snew (isize, ng);
- snew (index, ng);
- snew (grpname, ng);
+ snew(isize, ng);
+ snew(index, ng);
+ snew(grpname, ng);
- fprintf (stderr, "\nSelect %d group%s\n", ng,
- ng == 1 ? "" : "s");
+ fprintf(stderr, "\nSelect %d group%s\n", ng, ng == 1 ? "" : "s");
if (fnTPS)
{
- get_index (&top.atoms, fnNDX, ng, isize, index, grpname);
+ get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
}
else
{
- rd_index (fnNDX, ng, isize, index, grpname);
+ rd_index(fnNDX, ng, isize, index, grpname);
}
/* The first time we read data is a little special */
- read_first_frame (oenv, &status, fnTRX, &fr, flags);
+ read_first_frame(oenv, &status, fnTRX, &fr, flags);
sf->total_n_atoms = fr.natoms;
- snew (red, ng);
- snew (index_atp, ng);
+ snew(red, ng);
+ snew(index_atp, ng);
r_tmp = std::max(box[XX][XX], box[YY][YY]);
r_tmp = std::max(box[ZZ][ZZ], r_tmp);
/* ref_k will be the reference momentum unit */
sf->n_angles = gmx::roundToInt(end_q / sf->ref_k);
- snew (sf->F, ng);
+ snew(sf->F, ng);
for (i = 0; i < ng; i++)
{
- snew (sf->F[i], sf->n_angles);
+ snew(sf->F[i], sf->n_angles);
}
for (i = 0; i < ng; i++)
{
- snew (red[i], isize[i]);
- rearrange_atoms (red[i], &fr, index[i], isize[i], &top, TRUE, gmx_sf);
- index_atp[i] = create_indexed_atom_type (red[i], isize[i]);
+ snew(red[i], isize[i]);
+ rearrange_atoms(red[i], &fr, index[i], isize[i], &top, TRUE, gmx_sf);
+ index_atp[i] = create_indexed_atom_type(red[i], isize[i]);
}
- sf_table = compute_scattering_factor_table (gmx_sf, static_cast<structure_factor_t *>(sf));
+ sf_table = compute_scattering_factor_table(gmx_sf, static_cast<structure_factor_t*>(sf));
/* This is the main loop over frames */
sf->nSteps++;
for (i = 0; i < ng; i++)
{
- rearrange_atoms (red[i], &fr, index[i], isize[i], &top, FALSE, gmx_sf);
+ rearrange_atoms(red[i], &fr, index[i], isize[i], &top, FALSE, gmx_sf);
- compute_structure_factor (static_cast<structure_factor_t *>(sf), box, red[i], isize[i],
- start_q, end_q, i, sf_table);
+ compute_structure_factor(static_cast<structure_factor_t*>(sf), box, red[i], isize[i],
+ start_q, end_q, i, sf_table);
}
}
- while (read_next_frame (oenv, status, &fr));
+ while (read_next_frame(oenv, status, &fr));
- save_data (static_cast<structure_factor_t *>(sf), fnXVG, ng, start_q, end_q, oenv);
+ save_data(static_cast<structure_factor_t*>(sf), fnXVG, ng, start_q, end_q, oenv);
sfree(a);
}
-extern void save_data (structure_factor_t *sft, const char *file, int ngrps,
- real start_q, real end_q, const gmx_output_env_t *oenv)
+extern void save_data(structure_factor_t* sft,
+ const char* file,
+ int ngrps,
+ real start_q,
+ real end_q,
+ const gmx_output_env_t* oenv)
{
- FILE *fp;
- int i, g = 0;
- double *tmp, polarization_factor, A;
+ FILE* fp;
+ int i, g = 0;
+ double *tmp, polarization_factor, A;
- structure_factor *sf = static_cast<structure_factor *>(sft);
+ structure_factor* sf = static_cast<structure_factor*>(sft);
- fp = xvgropen (file, "Scattering Intensity", "q (1/nm)",
- "Intensity (a.u.)", oenv);
+ fp = xvgropen(file, "Scattering Intensity", "q (1/nm)", "Intensity (a.u.)", oenv);
- snew (tmp, ngrps);
+ snew(tmp, ngrps);
for (g = 0; g < ngrps; g++)
{
for (i = 0; i < sf->n_angles; i++)
{
-/*
- * theta is half the angle between incoming and scattered vectors.
- *
- * polar. fact. = 0.5*(1+cos^2(2*theta)) = 1 - 0.5 * sin^2(2*theta)
- *
- * sin(theta) = q/(2k) := A -> sin^2(theta) = 4*A^2 (1-A^2) ->
- * -> 0.5*(1+cos^2(2*theta)) = 1 - 2 A^2 (1-A^2)
- */
+ /*
+ * theta is half the angle between incoming and scattered vectors.
+ *
+ * polar. fact. = 0.5*(1+cos^2(2*theta)) = 1 - 0.5 * sin^2(2*theta)
+ *
+ * sin(theta) = q/(2k) := A -> sin^2(theta) = 4*A^2 (1-A^2) ->
+ * -> 0.5*(1+cos^2(2*theta)) = 1 - 2 A^2 (1-A^2)
+ */
A = static_cast<double>(i * sf->ref_k) / (2.0 * sf->momentum);
polarization_factor = 1 - 2.0 * gmx::square(A) * (1 - gmx::square(A));
- sf->F[g][i] *= polarization_factor;
+ sf->F[g][i] *= polarization_factor;
}
}
for (i = 0; i < sf->n_angles; i++)
{
if (i * sf->ref_k >= start_q && i * sf->ref_k <= end_q)
{
- fprintf (fp, "%10.5f ", i * sf->ref_k);
+ fprintf(fp, "%10.5f ", i * sf->ref_k);
for (g = 0; g < ngrps; g++)
{
- fprintf (fp, " %10.5f ", (sf->F[g][i]) /( sf->total_n_atoms*
- sf->nSteps));
+ fprintf(fp, " %10.5f ", (sf->F[g][i]) / (sf->total_n_atoms * sf->nSteps));
}
- fprintf (fp, "\n");
+ fprintf(fp, "\n");
}
}
- xvgrclose (fp);
+ xvgrclose(fp);
}
-extern double CMSF (gmx_structurefactors_t *gsf, int type, int nh, double lambda, double sin_theta)
+extern double CMSF(gmx_structurefactors_t* gsf, int type, int nh, double lambda, double sin_theta)
/*
* return Cromer-Mann fit for the atomic scattering factor:
* sin_theta is the sine of half the angle between incoming and scattered
{
int i;
double tmp = 0.0, k2;
- real *a, *b;
+ real * a, *b;
real c;
snew(a, 4);
*/
if (nh > 0)
{
- tmp = (CMSF (gsf, return_atom_type ("C", gsf), 0, lambda, sin_theta) +
- nh*CMSF (gsf, return_atom_type ("H", gsf), 0, lambda, sin_theta));
+ tmp = (CMSF(gsf, return_atom_type("C", gsf), 0, lambda, sin_theta)
+ + nh * CMSF(gsf, return_atom_type("H", gsf), 0, lambda, sin_theta));
}
/* all atom case */
else
{
- k2 = (gmx::square(sin_theta) / gmx::square(10.0 * lambda));
+ k2 = (gmx::square(sin_theta) / gmx::square(10.0 * lambda));
gmx_structurefactors_get_sf(gsf, type, a, b, &c);
- tmp = c;
+ tmp = c;
for (i = 0; (i < 4); i++)
{
- tmp += a[i] * exp (-b[i] * k2);
+ tmp += a[i] * exp(-b[i] * k2);
}
}
return tmp;
}
-
-extern real **gmx_structurefactors_table(gmx_structurefactors_t *gsf, real momentum, real ref_k, real lambda, int n_angles)
+extern real** gmx_structurefactors_table(gmx_structurefactors_t* gsf, real momentum, real ref_k, real lambda, int n_angles)
{
int NCMT;
int nsftable;
int i, j;
double q, sin_theta;
- real **sf_table;
- gmx_structurefactors *gsft = static_cast<gmx_structurefactors *>(gsf);
+ real** sf_table;
+ gmx_structurefactors* gsft = static_cast<gmx_structurefactors*>(gsf);
NCMT = gsft->nratoms;
- nsftable = NCMT+3;
+ nsftable = NCMT + 3;
- snew (sf_table, nsftable);
+ snew(sf_table, nsftable);
for (i = 0; (i < nsftable); i++)
{
- snew (sf_table[i], n_angles);
+ snew(sf_table[i], n_angles);
for (j = 0; j < n_angles; j++)
{
q = static_cast<double>(j * ref_k);
sin_theta = q / (2.0 * momentum);
if (i < NCMT)
{
- sf_table[i][j] = CMSF (gsf, i, 0, lambda, sin_theta);
+ sf_table[i][j] = CMSF(gsf, i, 0, lambda, sin_theta);
}
else
{
- sf_table[i][j] = CMSF (gsf, i, i-NCMT+1, lambda, sin_theta);
+ sf_table[i][j] = CMSF(gsf, i, i - NCMT + 1, lambda, sin_theta);
}
}
}
return sf_table;
}
-extern void gmx_structurefactors_done(gmx_structurefactors_t *gsf)
+extern void gmx_structurefactors_done(gmx_structurefactors_t* gsf)
{
int i;
- gmx_structurefactors *sf;
- sf = static_cast<gmx_structurefactors *>(gsf);
+ gmx_structurefactors* sf;
+ sf = static_cast<gmx_structurefactors*>(gsf);
for (i = 0; i < sf->nratoms; i++)
{
sfree(sf->c);
sfree(sf);
-
}
-extern real **compute_scattering_factor_table (gmx_structurefactors_t *gsf, structure_factor_t *sft)
+extern real** compute_scattering_factor_table(gmx_structurefactors_t* gsf, structure_factor_t* sft)
{
-/*
- * this function build up a table of scattering factors for every atom
- * type and for every scattering angle.
- */
+ /*
+ * this function build up a table of scattering factors for every atom
+ * type and for every scattering angle.
+ */
- double hc = 1239.842;
- real ** sf_table;
+ double hc = 1239.842;
+ real** sf_table;
- structure_factor *sf = static_cast<structure_factor *>(sft);
+ structure_factor* sf = static_cast<structure_factor*>(sft);
/* \hbar \omega \lambda = hc = 1239.842 eV * nm */
sf->momentum = (static_cast<double>(2. * 1000.0 * M_PI * sf->energy) / hc);
sf->lambda = hc / (1000.0 * sf->energy);
- fprintf (stderr, "\nwavelenght = %f nm\n", sf->lambda);
+ fprintf(stderr, "\nwavelenght = %f nm\n", sf->lambda);
sf_table = gmx_structurefactors_table(gsf, sf->momentum, sf->ref_k, sf->lambda, sf->n_angles);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff