aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/cell.c
diff options
context:
space:
mode:
Diffstat (limited to 'libcrystfel/src/cell.c')
-rw-r--r--libcrystfel/src/cell.c838
1 files changed, 275 insertions, 563 deletions
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 3d2a28bf..e7c9dace 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -1,7 +1,7 @@
/*
* cell.c
*
- * Unit Cell Calculations
+ * A class representing a unit cell
*
* Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
@@ -60,10 +60,6 @@
*/
-
-/* Weighting factor of lengths relative to angles */
-#define LWEIGHT (10.0e-9)
-
typedef enum {
CELL_REP_CRYST,
CELL_REP_CART,
@@ -92,8 +88,10 @@ struct _unitcell {
double ays; double bys; double cys;
double azs; double bzs; double czs;
- char *pointgroup;
- char *spacegroup;
+ char *pointgroup;
+ LatticeType lattice_type;
+ char centering;
+ char unique_axis;
};
@@ -125,7 +123,9 @@ UnitCell *cell_new()
cell->rep = CELL_REP_CRYST;
cell->pointgroup = strdup("1");
- cell->spacegroup = strdup("P 1");
+ cell->lattice_type = L_TRICLINIC;
+ cell->centering = 'P';
+ cell->unique_axis = 'c';
return cell;
}
@@ -142,7 +142,6 @@ void cell_free(UnitCell *cell)
{
if ( cell == NULL ) return;
free(cell->pointgroup);
- free(cell->spacegroup);
free(cell);
}
@@ -261,7 +260,9 @@ UnitCell *cell_new_from_cell(UnitCell *orig)
cell_get_cartesian(orig, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
cell_set_cartesian(new, ax, ay, az, bx, by, bz, cx, cy, cz);
cell_set_pointgroup(new, orig->pointgroup);
- cell_set_spacegroup(new, orig->spacegroup);
+ cell_set_lattice_type(new, orig->lattice_type);
+ cell_set_centering(new, orig->centering);
+ cell_set_unique_axis(new, orig->unique_axis);
return new;
}
@@ -282,17 +283,28 @@ void cell_set_reciprocal(UnitCell *cell,
}
-void cell_set_spacegroup(UnitCell *cell, const char *sym)
+void cell_set_pointgroup(UnitCell *cell, const char *sym)
{
- free(cell->spacegroup);
- cell->spacegroup = strdup(sym);
+ free(cell->pointgroup);
+ cell->pointgroup = strdup(sym);
}
-void cell_set_pointgroup(UnitCell *cell, const char *sym)
+void cell_set_centering(UnitCell *cell, char centering)
{
- free(cell->pointgroup);
- cell->pointgroup = strdup(sym);
+ cell->centering = centering;
+}
+
+
+void cell_set_lattice_type(UnitCell *cell, LatticeType lattice_type)
+{
+ cell->lattice_type = lattice_type;
+}
+
+
+void cell_set_unique_axis(UnitCell *cell, char unique_axis)
+{
+ cell->unique_axis = unique_axis;
}
@@ -555,18 +567,25 @@ const char *cell_get_pointgroup(UnitCell *cell)
}
-const char *cell_get_spacegroup(UnitCell *cell)
+char cell_get_centering(UnitCell *cell)
{
- return cell->spacegroup;
+ return cell->centering;
}
+LatticeType cell_get_lattice_type(UnitCell *cell)
+{
+ return cell->lattice_type;
+}
+char cell_get_unique_axis(UnitCell *cell)
+{
+ return cell->unique_axis;
+}
-/********************************* Utilities **********************************/
-static const char *cell_rep(UnitCell *cell)
+const char *cell_rep(UnitCell *cell)
{
switch ( cell->rep ) {
@@ -585,614 +604,307 @@ static const char *cell_rep(UnitCell *cell)
}
+struct _unitcelltransformation
+{
+ gsl_matrix *m;
+};
+
+
/**
- * cell_rotate:
- * @in: A %UnitCell to rotate
- * @quat: A %quaternion
+ * tfn_inverse:
+ * @t: A %UnitCellTransformation.
*
- * Rotate a %UnitCell using a %quaternion.
+ * Calculates the inverse of @t. That is, if you apply cell_transform() to a
+ * %UnitCell using @t, and then apply cell_transform() to the result using
+ * tfn_inverse(@t) instead of @t, you will recover the same lattice vectors
+ * (but note that the lattice type, centering and unique axis information will
+ * be lost).
*
- * Returns: a newly allocated rotated copy of @in.
+ * Returns: The inverse of @t.
*
*/
-UnitCell *cell_rotate(UnitCell *in, struct quaternion quat)
-{
- struct rvec a, b, c;
- struct rvec an, bn, cn;
- UnitCell *out = cell_new_from_cell(in);
-
- cell_get_cartesian(in, &a.u, &a.v, &a.w,
- &b.u, &b.v, &b.w,
- &c.u, &c.v, &c.w);
-
- an = quat_rot(a, quat);
- bn = quat_rot(b, quat);
- cn = quat_rot(c, quat);
-
- cell_set_cartesian(out, an.u, an.v, an.w,
- bn.u, bn.v, bn.w,
- cn.u, cn.v, cn.w);
-
- return out;
-}
-
-
-void cell_print(UnitCell *cell)
+UnitCellTransformation *tfn_inverse(UnitCellTransformation *t)
{
- double asx, asy, asz;
- double bsx, bsy, bsz;
- double csx, csy, csz;
- double a, b, c, alpha, beta, gamma;
- double ax, ay, az, bx, by, bz, cx, cy, cz;
-
- cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
-
- STATUS(" a b c alpha beta gamma\n");
- STATUS("%5.2f %5.2f %5.2f nm %6.2f %6.2f %6.2f deg\n",
- a*1e9, b*1e9, c*1e9,
- rad2deg(alpha), rad2deg(beta), rad2deg(gamma));
-
- cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-
- STATUS("a = %10.3e %10.3e %10.3e m\n", ax, ay, az);
- STATUS("b = %10.3e %10.3e %10.3e m\n", bx, by, bz);
- STATUS("c = %10.3e %10.3e %10.3e m\n", cx, cy, cz);
-
- cell_get_reciprocal(cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz);
-
- STATUS("astar = %10.3e %10.3e %10.3e m^-1 (modulus = %10.3e m^-1)\n",
- asx, asy, asz, modulus(asx, asy, asz));
- STATUS("bstar = %10.3e %10.3e %10.3e m^-1 (modulus = %10.3e m^-1)\n",
- bsx, bsy, bsz, modulus(bsx, bsy, bsz));
- STATUS("cstar = %10.3e %10.3e %10.3e m^-1 (modulus = %10.3e m^-1)\n",
- csx, csy, csz, modulus(csx, csy, csz));
-
- STATUS("Point group: %s\n", cell_get_pointgroup(cell));
- STATUS("Cell representation is %s.\n", cell_rep(cell));
-}
-
-
-#define MAX_CAND (1024)
-
-static int right_handed(struct rvec a, struct rvec b, struct rvec c)
-{
- struct rvec aCb;
- double aCb_dot_c;
-
- /* "a" cross "b" */
- aCb.u = a.v*b.w - a.w*b.v;
- aCb.v = - (a.u*b.w - a.w*b.u);
- aCb.w = a.u*b.v - a.v*b.u;
-
- /* "a cross b" dot "c" */
- aCb_dot_c = aCb.u*c.u + aCb.v*c.v + aCb.w*c.w;
-
- if ( aCb_dot_c > 0.0 ) return 1;
- return 0;
-}
-
-
-struct cvec {
- struct rvec vec;
- float na;
- float nb;
- float nc;
- float fom;
-};
-
-
-static int same_vector(struct cvec a, struct cvec b)
-{
- if ( a.na != b.na ) return 0;
- if ( a.nb != b.nb ) return 0;
- if ( a.nc != b.nc ) return 0;
- return 1;
-}
+ int s;
+ gsl_matrix *m;
+ gsl_matrix *inv;
+ gsl_permutation *perm;
+ UnitCellTransformation *out;
+ m = gsl_matrix_alloc(3, 3);
+ if ( m == NULL ) return NULL;
-/* Attempt to make 'cell' fit into 'template' somehow */
-UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose,
- const float *tols, int reduce)
-{
- signed int n1l, n2l, n3l;
- double asx, asy, asz;
- double bsx, bsy, bsz;
- double csx, csy, csz;
- int i, j;
- double lengths[3];
- double angles[3];
- struct cvec *cand[3];
- UnitCell *new_cell = NULL;
- float best_fom = +999999999.9; /* Large number.. */
- int ncand[3] = {0,0,0};
- signed int ilow, ihigh;
- float angtol = deg2rad(tols[3]);
-
- if ( cell_get_reciprocal(template, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz) ) {
- ERROR("Couldn't get reciprocal cell for template.\n");
+ out = tfn_identity();
+ if ( out == NULL ) {
+ gsl_matrix_free(m);
return NULL;
}
- lengths[0] = modulus(asx, asy, asz);
- lengths[1] = modulus(bsx, bsy, bsz);
- lengths[2] = modulus(csx, csy, csz);
-
- angles[0] = angle_between(bsx, bsy, bsz, csx, csy, csz);
- angles[1] = angle_between(asx, asy, asz, csx, csy, csz);
- angles[2] = angle_between(asx, asy, asz, bsx, bsy, bsz);
+ gsl_matrix_memcpy(m, t->m);
- cand[0] = malloc(MAX_CAND*sizeof(struct cvec));
- cand[1] = malloc(MAX_CAND*sizeof(struct cvec));
- cand[2] = malloc(MAX_CAND*sizeof(struct cvec));
-
- if ( cell_get_reciprocal(cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz) ) {
- ERROR("Couldn't get reciprocal cell.\n");
+ perm = gsl_permutation_alloc(m->size1);
+ if ( perm == NULL ) {
+ ERROR("Couldn't allocate permutation\n");
return NULL;
}
-
- if ( reduce ) {
- ilow = -2; ihigh = 4;
- } else {
- ilow = 0; ihigh = 1;
- }
-
- /* Negative values mean 1/n, positive means n, zero means zero */
- for ( n1l=ilow; n1l<=ihigh; n1l++ ) {
- for ( n2l=ilow; n2l<=ihigh; n2l++ ) {
- for ( n3l=ilow; n3l<=ihigh; n3l++ ) {
-
- float n1, n2, n3;
- signed int b1, b2, b3;
-
- n1 = (n1l>=0) ? (n1l) : (1.0/n1l);
- n2 = (n2l>=0) ? (n2l) : (1.0/n2l);
- n3 = (n3l>=0) ? (n3l) : (1.0/n3l);
-
- if ( !reduce ) {
- if ( n1l + n2l + n3l > 1 ) continue;
- }
-
- /* 'bit' values can be +1 or -1 */
- for ( b1=-1; b1<=1; b1+=2 ) {
- for ( b2=-1; b2<=1; b2+=2 ) {
- for ( b3=-1; b3<=1; b3+=2 ) {
-
- double tx, ty, tz;
- double tlen;
- int i;
-
- n1 *= b1; n2 *= b2; n3 *= b3;
-
- tx = n1*asx + n2*bsx + n3*csx;
- ty = n1*asy + n2*bsy + n3*csy;
- tz = n1*asz + n2*bsz + n3*csz;
- tlen = modulus(tx, ty, tz);
-
- /* Test modulus for agreement with moduli of template */
- for ( i=0; i<3; i++ ) {
-
- if ( !within_tolerance(lengths[i], tlen,
- tols[i]) )
- {
- continue;
- }
-
- if ( ncand[i] == MAX_CAND ) {
- ERROR("Too many cell candidates - ");
- ERROR("consider tightening the unit ");
- ERROR("cell tolerances.\n");
- } else {
-
- double fom;
-
- fom = fabs(lengths[i] - tlen);
-
- cand[i][ncand[i]].vec.u = tx;
- cand[i][ncand[i]].vec.v = ty;
- cand[i][ncand[i]].vec.w = tz;
- cand[i][ncand[i]].na = n1;
- cand[i][ncand[i]].nb = n2;
- cand[i][ncand[i]].nc = n3;
- cand[i][ncand[i]].fom = fom;
-
- ncand[i]++;
-
- }
-
- }
-
- }
- }
- }
-
- }
- }
- }
-
- if ( verbose ) {
- STATUS("Candidates: %i %i %i\n", ncand[0], ncand[1], ncand[2]);
+ inv = gsl_matrix_alloc(m->size1, m->size2);
+ if ( inv == NULL ) {
+ ERROR("Couldn't allocate inverse\n");
+ gsl_permutation_free(perm);
+ return NULL;
}
-
- for ( i=0; i<ncand[0]; i++ ) {
- for ( j=0; j<ncand[1]; j++ ) {
-
- double ang;
- int k;
- float fom1;
-
- if ( same_vector(cand[0][i], cand[1][j]) ) continue;
-
- /* Measure the angle between the ith candidate for axis 0
- * and the jth candidate for axis 1 */
- ang = angle_between(cand[0][i].vec.u, cand[0][i].vec.v,
- cand[0][i].vec.w, cand[1][j].vec.u,
- cand[1][j].vec.v, cand[1][j].vec.w);
-
- /* Angle between axes 0 and 1 should be angle 2 */
- if ( fabs(ang - angles[2]) > angtol ) continue;
-
- fom1 = fabs(ang - angles[2]);
-
- for ( k=0; k<ncand[2]; k++ ) {
-
- float fom2, fom3;
-
- if ( same_vector(cand[1][j], cand[2][k]) ) continue;
-
- /* Measure the angle between the current candidate for
- * axis 0 and the kth candidate for axis 2 */
- ang = angle_between(cand[0][i].vec.u, cand[0][i].vec.v,
- cand[0][i].vec.w, cand[2][k].vec.u,
- cand[2][k].vec.v, cand[2][k].vec.w);
-
- /* ... it should be angle 1 ... */
- if ( fabs(ang - angles[1]) > angtol ) continue;
-
- fom2 = fom1 + fabs(ang - angles[1]);
-
- /* Finally, the angle between the current candidate for
- * axis 1 and the kth candidate for axis 2 */
- ang = angle_between(cand[1][j].vec.u, cand[1][j].vec.v,
- cand[1][j].vec.w, cand[2][k].vec.u,
- cand[2][k].vec.v, cand[2][k].vec.w);
-
- /* ... it should be angle 0 ... */
- if ( fabs(ang - angles[0]) > angtol ) continue;
-
- /* Unit cell must be right-handed */
- if ( !right_handed(cand[0][i].vec, cand[1][j].vec,
- cand[2][k].vec) ) continue;
-
- fom3 = fom2 + fabs(ang - angles[0]);
- fom3 += LWEIGHT * (cand[0][i].fom + cand[1][j].fom
- + cand[2][k].fom);
-
- if ( fom3 < best_fom ) {
- if ( new_cell != NULL ) free(new_cell);
- new_cell = cell_new_from_reciprocal_axes(
- cand[0][i].vec, cand[1][j].vec,
- cand[2][k].vec);
- best_fom = fom3;
- }
-
- }
-
+ if ( gsl_linalg_LU_decomp(m, perm, &s) ) {
+ ERROR("Couldn't decompose matrix\n");
+ gsl_permutation_free(perm);
+ return NULL;
}
+ if ( gsl_linalg_LU_invert(m, perm, inv) ) {
+ ERROR("Couldn't invert matrix\n");
+ gsl_permutation_free(perm);
+ return NULL;
}
+ gsl_permutation_free(perm);
- free(cand[0]);
- free(cand[1]);
- free(cand[2]);
-
- return new_cell;
+ gsl_matrix_free(out->m);
+ gsl_matrix_free(m);
+ out->m = inv;
+ return out;
}
-
-UnitCell *match_cell_ab(UnitCell *cell, UnitCell *template)
+/**
+ * cell_transform:
+ * @cell: A %UnitCell.
+ * @t: A %UnitCellTransformation.
+ *
+ * Applies @t to @cell. Note that the lattice type, centering and unique axis
+ * information will not be preserved.
+ *
+ * Returns: Transformed copy of @cell.
+ *
+ */
+UnitCell *cell_transform(UnitCell *cell, UnitCellTransformation *t)
{
+ UnitCell *out;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
- int i;
- double lengths[3];
- int used[3];
- struct rvec real_a, real_b, real_c;
- struct rvec params[3];
- double alen, blen;
- float ltl = 5.0; /* percent */
- int have_real_a;
- int have_real_b;
- int have_real_c;
-
- /* Get the lengths to match */
- if ( cell_get_cartesian(template, &ax, &ay, &az,
- &bx, &by, &bz,
- &cx, &cy, &cz) )
- {
- ERROR("Couldn't get cell for template.\n");
- return NULL;
- }
- alen = modulus(ax, ay, az);
- blen = modulus(bx, by, bz);
-
- /* Get the lengths from the cell and turn them into anonymous vectors */
- if ( cell_get_cartesian(cell, &ax, &ay, &az,
- &bx, &by, &bz,
- &cx, &cy, &cz) )
- {
- ERROR("Couldn't get cell.\n");
- return NULL;
- }
- lengths[0] = modulus(ax, ay, az);
- lengths[1] = modulus(bx, by, bz);
- lengths[2] = modulus(cx, cy, cz);
- used[0] = 0; used[1] = 0; used[2] = 0;
- params[0].u = ax; params[0].v = ay; params[0].w = az;
- params[1].u = bx; params[1].v = by; params[1].w = bz;
- params[2].u = cx; params[2].v = cy; params[2].w = cz;
-
- real_a.u = 0.0; real_a.v = 0.0; real_a.w = 0.0;
- real_b.u = 0.0; real_b.v = 0.0; real_b.w = 0.0;
- real_c.u = 0.0; real_c.v = 0.0; real_c.w = 0.0;
-
- /* Check each vector against a and b */
- have_real_a = 0;
- have_real_b = 0;
- for ( i=0; i<3; i++ ) {
- if ( within_tolerance(lengths[i], alen, ltl)
- && !used[i] && !have_real_a )
- {
- used[i] = 1;
- memcpy(&real_a, &params[i], sizeof(struct rvec));
- have_real_a = 1;
- }
- if ( within_tolerance(lengths[i], blen, ltl)
- && !used[i] && !have_real_b )
- {
- used[i] = 1;
- memcpy(&real_b, &params[i], sizeof(struct rvec));
- have_real_b = 1;
- }
- }
+ gsl_matrix *m;
+ gsl_matrix *a;
- /* Have we matched both a and b? */
- if ( !(have_real_a && have_real_b) ) return NULL;
+ if ( t == NULL ) return NULL;
- /* "c" is "the other one" */
- have_real_c = 0;
- for ( i=0; i<3; i++ ) {
- if ( !used[i] ) {
- memcpy(&real_c, &params[i], sizeof(struct rvec));
- have_real_c = 1;
- }
- }
+ out = cell_new_from_cell(cell);
+ if ( out == NULL ) return NULL;
- if ( !have_real_c ) {
- ERROR("Huh? Couldn't find the third vector.\n");
- ERROR("Matches: %i %i %i\n", used[0], used[1], used[2]);
- return NULL;
- }
+ cell_get_cartesian(out, &ax, &ay, &az,
+ &bx, &by, &bz,
+ &cx, &cy, &cz);
- /* Flip c if not right-handed */
- if ( !right_handed(real_a, real_b, real_c) ) {
- real_c.u = -real_c.u;
- real_c.v = -real_c.v;
- real_c.w = -real_c.w;
+ m = gsl_matrix_alloc(3,3);
+ a = gsl_matrix_calloc(3,3);
+ if ( (m == NULL) || (a == NULL) ) {
+ cell_free(out);
+ return NULL;
}
- return cell_new_from_direct_axes(real_a, real_b, real_c);
-}
-
-
-/* Return sin(theta)/lambda = 1/2d. Multiply by two if you want 1/d */
-double resolution(UnitCell *cell, signed int h, signed int k, signed int l)
-{
- double a, b, c, alpha, beta, gamma;
-
- cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
+ gsl_matrix_set(m, 0, 0, ax);
+ gsl_matrix_set(m, 0, 1, ay);
+ gsl_matrix_set(m, 0, 2, az);
+ gsl_matrix_set(m, 1, 0, bx);
+ gsl_matrix_set(m, 1, 1, by);
+ gsl_matrix_set(m, 1, 2, bz);
+ gsl_matrix_set(m, 2, 0, cx);
+ gsl_matrix_set(m, 2, 1, cy);
+ gsl_matrix_set(m, 2, 2, cz);
- const double Vsq = a*a*b*b*c*c*(1 - cos(alpha)*cos(alpha)
- - cos(beta)*cos(beta)
- - cos(gamma)*cos(gamma)
- + 2*cos(alpha)*cos(beta)*cos(gamma) );
+ gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, t->m, m, 1.0, a);
- const double S11 = b*b*c*c*sin(alpha)*sin(alpha);
- const double S22 = a*a*c*c*sin(beta)*sin(beta);
- const double S33 = a*a*b*b*sin(gamma)*sin(gamma);
- const double S12 = a*b*c*c*(cos(alpha)*cos(beta) - cos(gamma));
- const double S23 = a*a*b*c*(cos(beta)*cos(gamma) - cos(alpha));
- const double S13 = a*b*b*c*(cos(gamma)*cos(alpha) - cos(beta));
+ cell_set_cartesian(out, gsl_matrix_get(a, 0, 0),
+ gsl_matrix_get(a, 0, 1),
+ gsl_matrix_get(a, 0, 2),
+ gsl_matrix_get(a, 1, 0),
+ gsl_matrix_get(a, 1, 1),
+ gsl_matrix_get(a, 1, 2),
+ gsl_matrix_get(a, 2, 0),
+ gsl_matrix_get(a, 2, 1),
+ gsl_matrix_get(a, 2, 2));
- const double brackets = S11*h*h + S22*k*k + S33*l*l
- + 2*S12*h*k + 2*S23*k*l + 2*S13*h*l;
- const double oneoverdsq = brackets / Vsq;
- const double oneoverd = sqrt(oneoverdsq);
+ gsl_matrix_free(a);
+ gsl_matrix_free(m);
- return oneoverd / 2;
+ return out;
}
-static void cell_set_pointgroup_from_pdb(UnitCell *cell, const char *sym)
+/**
+ * cell_transform_inverse:
+ * @cell: A %UnitCell.
+ * @t: A %UnitCellTransformation.
+ *
+ * Applies the inverse of @t to @cell.
+ *
+ * Returns: Transformed copy of @cell.
+ *
+ */
+UnitCell *cell_transform_inverse(UnitCell *cell, UnitCellTransformation *t)
{
- char *new = NULL;
-
- if ( strcmp(sym, "P 1") == 0 ) new = "1";
- if ( strcmp(sym, "P 63") == 0 ) new = "6";
- if ( strcmp(sym, "P 21 21 21") == 0 ) new = "222";
- if ( strcmp(sym, "P 2 2 2") == 0 ) new = "222";
- if ( strcmp(sym, "P 43 21 2") == 0 ) new = "422";
-
- if ( new != NULL ) {
- cell_set_pointgroup(cell, new);
- } else {
- ERROR("Can't determine point group for '%s'\n", sym);
- }
+ UnitCellTransformation *inv;
+ UnitCell *out;
+
+ inv = tfn_inverse(t);
+ out = cell_transform(cell, inv);
+ tfn_free(inv);
+ return out;
}
-UnitCell *load_cell_from_pdb(const char *filename)
+/**
+ * tfn_identity:
+ *
+ * Returns: A %UnitCellTransformation corresponding to an identity operation.
+ *
+ */
+UnitCellTransformation *tfn_identity()
{
- FILE *fh;
- char *rval;
- UnitCell *cell = NULL;
+ UnitCellTransformation *tfn;
+
+ tfn = calloc(1, sizeof(UnitCellTransformation));
+ if ( tfn == NULL ) return NULL;
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- ERROR("Couldn't open '%s'\n", filename);
+ tfn->m = gsl_matrix_alloc(3, 3);
+ if ( tfn->m == NULL ) {
+ free(tfn);
return NULL;
}
- do {
+ gsl_matrix_set_identity(tfn->m);
- char line[1024];
-
- rval = fgets(line, 1023, fh);
-
- if ( strncmp(line, "CRYST1", 6) == 0 ) {
-
- float a, b, c, al, be, ga;
- char as[10], bs[10], cs[10];
- char als[8], bes[8], gas[8];
- char *sym;
- int r;
-
- memcpy(as, line+6, 9); as[9] = '\0';
- memcpy(bs, line+15, 9); bs[9] = '\0';
- memcpy(cs, line+24, 9); cs[9] = '\0';
- memcpy(als, line+33, 7); als[7] = '\0';
- memcpy(bes, line+40, 7); bes[7] = '\0';
- memcpy(gas, line+47, 7); gas[7] = '\0';
-
- r = sscanf(as, "%f", &a);
- r += sscanf(bs, "%f", &b);
- r += sscanf(cs, "%f", &c);
- r += sscanf(als, "%f", &al);
- r += sscanf(bes, "%f", &be);
- r += sscanf(gas, "%f", &ga);
-
- if ( r != 6 ) {
- STATUS("Couldn't understand CRYST1 line.\n");
- continue;
- }
+ return tfn;
+}
- cell = cell_new_from_parameters(a*1e-10,
- b*1e-10, c*1e-10,
- deg2rad(al),
- deg2rad(be),
- deg2rad(ga));
- if ( strlen(line) > 65 ) {
- sym = strndup(line+55, 10);
- notrail(sym);
- cell_set_pointgroup_from_pdb(cell, sym);
- cell_set_spacegroup(cell, sym);
- free(sym);
- } else {
- cell_set_pointgroup_from_pdb(cell, "P 1");
- cell_set_spacegroup(cell, "P 1");
- ERROR("CRYST1 line without space group.\n");
- }
+/**
+ * tfn_combine:
+ * @t: A %UnitCellTransformation
+ * @na: Pointer to three doubles representing naa, nab, nac
+ * @nb: Pointer to three doubles representing nba, nbb, nbc
+ * @nc: Pointer to three doubles representing nca, ncb, ncc
+ *
+ * Updates @t such that it represents its previous transformation followed by
+ * a new transformation, corresponding to letting a = naa*a + nab*b + nac*c.
+ * Likewise, a = nba*a + nbb*b + nbc*c and c = nca*a + ncb*b + ncc*c.
+ *
+ */
+void tfn_combine(UnitCellTransformation *t, double *na, double *nb, double *nc)
+{
+ gsl_matrix *a;
+ gsl_matrix *n;
- break; /* Done */
- }
+ n = gsl_matrix_alloc(3, 3);
+ a = gsl_matrix_calloc(3, 3);
+ if ( (n == NULL) || (a == NULL) ) {
+ return;
+ }
+ gsl_matrix_set(n, 0, 0, na[0]);
+ gsl_matrix_set(n, 0, 1, na[1]);
+ gsl_matrix_set(n, 0, 2, na[2]);
+ gsl_matrix_set(n, 1, 0, nb[0]);
+ gsl_matrix_set(n, 1, 1, nb[1]);
+ gsl_matrix_set(n, 1, 2, nb[2]);
+ gsl_matrix_set(n, 2, 0, nc[0]);
+ gsl_matrix_set(n, 2, 1, nc[1]);
+ gsl_matrix_set(n, 2, 2, nc[2]);
- } while ( rval != NULL );
+ free(na);
+ free(nb);
+ free(nc);
- fclose(fh);
+ gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, n, t->m, 1.0, a);
- return cell;
+ gsl_matrix_free(t->m);
+ t->m = a;
+ gsl_matrix_free(n);
}
-/* Force the linker to bring in CBLAS to make GSL happy */
-void cell_fudge_gslcblas()
+/**
+ * tfn_vector:
+ * @a: Amount of "a" to include in new vector
+ * @b: Amount of "b" to include in new vector
+ * @c: Amount of "c" to include in new vector
+ *
+ * This is a convenience function to use when sending vectors to tfn_combine():
+ * tfn_combine(tfn, tfn_vector(1,0,0),
+ * tfn_vector(0,2,0),
+ * tfn_vector(0,0,1));
+ *
+ */
+double *tfn_vector(double a, double b, double c)
{
- STATUS("%p\n", cblas_sgemm);
+ double *vec = malloc(3*sizeof(double));
+ if ( vec == NULL ) return NULL;
+ vec[0] = a; vec[1] = b; vec[2] = c;
+ return vec;
}
-UnitCell *rotate_cell(UnitCell *in, double omega, double phi, double rot)
+/**
+ * tfn_print:
+ * @t: A %UnitCellTransformation
+ *
+ * Prints information about @t to stderr.
+ *
+ */
+void tfn_print(UnitCellTransformation *t)
{
- UnitCell *out;
- double asx, asy, asz;
- double bsx, bsy, bsz;
- double csx, csy, csz;
- double xnew, ynew, znew;
-
- cell_get_reciprocal(in, &asx, &asy, &asz, &bsx, &bsy,
- &bsz, &csx, &csy, &csz);
-
- /* Rotate by "omega" about +z (parallel to c* and c unless triclinic) */
- xnew = asx*cos(omega) + asy*sin(omega);
- ynew = -asx*sin(omega) + asy*cos(omega);
- znew = asz;
- asx = xnew; asy = ynew; asz = znew;
- xnew = bsx*cos(omega) + bsy*sin(omega);
- ynew = -bsx*sin(omega) + bsy*cos(omega);
- znew = bsz;
- bsx = xnew; bsy = ynew; bsz = znew;
- xnew = csx*cos(omega) + csy*sin(omega);
- ynew = -csx*sin(omega) + csy*cos(omega);
- znew = csz;
- csx = xnew; csy = ynew; csz = znew;
-
- /* Rotate by "phi" about +x (not parallel to anything specific) */
- xnew = asx;
- ynew = asy*cos(phi) + asz*sin(phi);
- znew = -asy*sin(phi) + asz*cos(phi);
- asx = xnew; asy = ynew; asz = znew;
- xnew = bsx;
- ynew = bsy*cos(phi) + bsz*sin(phi);
- znew = -bsy*sin(phi) + bsz*cos(phi);
- bsx = xnew; bsy = ynew; bsz = znew;
- xnew = csx;
- ynew = csy*cos(phi) + csz*sin(phi);
- znew = -csy*sin(phi) + csz*cos(phi);
- csx = xnew; csy = ynew; csz = znew;
-
- /* Rotate by "rot" about the new +z (in-plane rotation) */
- xnew = asx*cos(rot) + asy*sin(rot);
- ynew = -asx*sin(rot) + asy*cos(rot);
- znew = asz;
- asx = xnew; asy = ynew; asz = znew;
- xnew = bsx*cos(rot) + bsy*sin(rot);
- ynew = -bsx*sin(rot) + bsy*cos(rot);
- znew = bsz;
- bsx = xnew; bsy = ynew; bsz = znew;
- xnew = csx*cos(rot) + csy*sin(rot);
- ynew = -csx*sin(rot) + csy*cos(rot);
- znew = csz;
- csx = xnew; csy = ynew; csz = znew;
-
- out = cell_new_from_cell(in);
- cell_set_reciprocal(out, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+ gsl_permutation *perm;
+ gsl_matrix *lu;
+ int s;
- return out;
+ STATUS("New a = %+.2fa %+.2fb %+.2fc\n", gsl_matrix_get(t->m, 0, 0),
+ gsl_matrix_get(t->m, 0, 1),
+ gsl_matrix_get(t->m, 0, 2));
+ STATUS("New b = %+.2fa %+.2fb %+.2fc\n", gsl_matrix_get(t->m, 1, 0),
+ gsl_matrix_get(t->m, 1, 1),
+ gsl_matrix_get(t->m, 1, 2));
+ STATUS("New c = %+.2fa %+.2fb %+.2fc\n", gsl_matrix_get(t->m, 2, 0),
+ gsl_matrix_get(t->m, 2, 1),
+ gsl_matrix_get(t->m, 2, 2));
+ lu = gsl_matrix_alloc(3, 3);
+ if ( lu == NULL ) {
+ ERROR("Couldn't allocate LU decomposition.\n");
+ return;
+ }
+
+ gsl_matrix_memcpy(lu, t->m);
+
+ perm = gsl_permutation_alloc(t->m->size1);
+ if ( perm == NULL ) {
+ ERROR("Couldn't allocate permutation.\n");
+ gsl_matrix_free(lu);
+ return;
+ }
+ if ( gsl_linalg_LU_decomp(lu, perm, &s) ) {
+ ERROR("LU decomposition failed.\n");
+ gsl_permutation_free(perm);
+ gsl_matrix_free(lu);
+ return;
+ }
+
+ STATUS("Transformation determinant = %.2f\n", gsl_linalg_LU_det(lu, s));
}
-int cell_is_sensible(UnitCell *cell)
+/**
+ * tfn_free:
+ * @t: A %UnitCellTransformation
+ *
+ * Frees all resources associated with @t.
+ *
+ */
+void tfn_free(UnitCellTransformation *t)
{
- double a, b, c, al, be, ga;
-
- cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
- if ( al + be + ga >= 2.0*M_PI ) return 0;
- if ( al + be - ga >= 2.0*M_PI ) return 0;
- if ( al - be + ga >= 2.0*M_PI ) return 0;
- if ( - al + be + ga >= 2.0*M_PI ) return 0;
- if ( al + be + ga <= 0.0 ) return 0;
- if ( al + be - ga <= 0.0 ) return 0;
- if ( al - be + ga <= 0.0 ) return 0;
- if ( - al + be + ga <= 0.0 ) return 0;
- if ( isnan(al) ) return 0;
- if ( isnan(be) ) return 0;
- if ( isnan(ga) ) return 0;
- return 1;
+ gsl_matrix_free(t->m);
+ free(t);
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-14 07:23:36 +0000