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authorThomas White <taw@physics.org>2011-07-18 17:23:29 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:33 +0100
commit33077f930ed81d70081a95edb7d7004390fa4047 (patch)
tree313478c0be82e77cea970de5cc6178d6391a1866
parentfc7e817ea9f833ea7eb2d11fcd58035398d365cd (diff)
New symmetry core done (gulp)
-rw-r--r--doc/reference/CrystFEL-sections.txt2
-rw-r--r--src/symmetry.c207
2 files changed, 168 insertions, 41 deletions
diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt
index b9135f1b..30fc8c5c 100644
--- a/doc/reference/CrystFEL-sections.txt
+++ b/doc/reference/CrystFEL-sections.txt
@@ -198,7 +198,7 @@ indexingprivate
SymOpList
<SUBSECTION>
free_symoplist
-num_ops
+num_equivs
get_pointgroup
get_equiv
special_position
diff --git a/src/symmetry.c b/src/symmetry.c
index bf67ec37..42c66193 100644
--- a/src/symmetry.c
+++ b/src/symmetry.c
@@ -18,6 +18,7 @@
#include <stdio.h>
#include <string.h>
#include <math.h>
+#include <assert.h>
#include "symmetry.h"
#include "utils.h"
@@ -54,8 +55,7 @@ struct sym_op
signed int *h;
signed int *k;
signed int *l; /* Contributions to h, k and l from h, k, i and l */
- enum lattice_type latt;
- char op[6];
+ int order;
};
@@ -122,33 +122,127 @@ void free_symoplist(SymOpList *ops)
}
+static int is_identity(signed int *h, signed int *k, signed int *l)
+{
+ if ( (h[0]!=1) || (h[1]!=0) || (h[2]!=0) ) return 0;
+ if ( (k[0]!=0) || (k[1]!=1) || (k[2]!=0) ) return 0;
+ if ( (l[0]!=0) || (l[1]!=0) || (l[2]!=1) ) return 0;
+ return 1;
+}
+
+
+/* Calculate the order of the operation "M", which is the lowest
+ * integer n such that M^n = I. */
+static int order_of_op(signed int *hin, signed int *kin, signed int *lin)
+{
+ int n;
+ signed int h[3];
+ signed int k[3];
+ signed int l[3];
+
+ memcpy(h, hin, 3*sizeof(signed int));
+ memcpy(k, kin, 3*sizeof(signed int));
+ memcpy(l, lin, 3*sizeof(signed int));
+
+ for ( n=1; n<6; n++ ) {
+
+ signed int hnew[3];
+ signed int knew[3];
+ signed int lnew[3];
+
+ /* Yay matrices */
+ hnew[0] = h[0]*h[0] + h[1]*k[0] + h[2]*l[0];
+ hnew[1] = h[0]*h[1] + h[1]*k[1] + h[2]*l[1];
+ hnew[2] = h[0]*h[2] + h[1]*k[2] + h[2]*l[2];
+
+ knew[0] = k[0]*h[0] + k[1]*k[0] + k[2]*l[0];
+ knew[1] = k[0]*h[1] + k[1]*k[1] + k[2]*l[1];
+ knew[2] = k[0]*h[2] + k[1]*k[2] + k[2]*l[2];
+
+ lnew[0] = l[0]*h[0] + l[1]*k[0] + l[2]*l[0];
+ lnew[1] = l[0]*h[1] + l[1]*k[1] + l[2]*l[1];
+ lnew[2] = l[0]*h[2] + l[1]*k[2] + l[2]*l[2];
+
+ if ( is_identity(hnew, knew, lnew) ) break;
+
+ memcpy(h, hnew, 3*sizeof(signed int));
+ memcpy(k, knew, 3*sizeof(signed int));
+ memcpy(l, lnew, 3*sizeof(signed int));
+
+ }
+
+ return n;
+}
+
+
/* Add a operation to a SymOpList */
static void add_symop(SymOpList *ops,
signed int *h, signed int *k, signed int *l)
{
+ int n;
+
if ( ops->n_ops == ops->max_ops ) {
/* Pretty sure this never happens, but still... */
ops->max_ops += 16;
alloc_ops(ops);
}
- ops->ops[ops->n_ops].h = h;
- ops->ops[ops->n_ops].k = k;
- ops->ops[ops->n_ops].l = l;
+ n = ops->n_ops;
+ ops->ops[n].h = h;
+ ops->ops[n].k = k;
+ ops->ops[n].l = l;
+ ops->ops[n].order = order_of_op(h, k, l);
ops->n_ops++;
}
-int num_ops(const SymOpList *ops)
+static void add_copied_symop(SymOpList *ops, struct sym_op *copyme)
+{
+ if ( ops->n_ops == ops->max_ops ) {
+ /* Pretty sure this never happens, but still... */
+ ops->max_ops += 16;
+ alloc_ops(ops);
+ }
+
+ memcpy(&ops->ops[ops->n_ops], copyme, sizeof(*copyme));
+ ops->n_ops++;
+}
+
+
+/* This returns the number of operations in "ops". To get the number of
+ * symmetric equivalents this generates, use num_equivs() instead. */
+static int num_ops(const SymOpList *ops)
{
return ops->n_ops;
}
+/**
+ * num_equivs:
+ *
+ * Returns: the number of equivalent reflections for a general reflection
+ * in point group "ops".
+ **/
+int num_equivs(const SymOpList *ops)
+{
+ int i, n, tot;
+
+ n = num_ops(ops);
+ tot = 1;
+
+ for ( i=0; i<n; i++ ) {
+ tot *= ops->ops[i].order;
+ }
+
+ return tot;
+}
+
+
static signed int *v(signed int h, signed int k, signed int i, signed int l)
{
- signed int *vec = malloc(4*sizeof(signed int));
- vec[0] = h; vec[1] = k; vec[2] = i; vec[3] = l;
+ signed int *vec = malloc(3*sizeof(signed int));
+ /* Convert back to 3-index form now */
+ vec[0] = h-i; vec[1] = k-i; vec[2] = l;
return vec;
}
@@ -158,8 +252,7 @@ static signed int *v(signed int h, signed int k, signed int i, signed int l)
static SymOpList *make_1bar()
{
SymOpList *new = new_symoplist();
- add_symop(new, v(1,0,0,0), v(0,1,0,0), v(0,0,0,1));
- add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,-1));
+ add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,-1)); /* -I */
return new;
}
@@ -167,7 +260,6 @@ static SymOpList *make_1bar()
static SymOpList *make_1()
{
SymOpList *new = new_symoplist();
- add_symop(new, v(1,0,0,0), v(0,1,0,0), v(0,0,0,1));
return new;
}
@@ -176,18 +268,25 @@ static SymOpList *make_1()
static SymOpList *make_2m()
{
+ SymOpList *new = new_symoplist();
+ add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
+ add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
return NULL;
}
static SymOpList *make_2()
{
+ SymOpList *new = new_symoplist();
+ add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
return NULL;
}
static SymOpList *make_m()
{
+ SymOpList *new = new_symoplist();
+ add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
return NULL;
}
@@ -196,18 +295,28 @@ static SymOpList *make_m()
static SymOpList *make_mmm()
{
+ SymOpList *new = new_symoplist();
+ add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* 2 */
+ add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
+ add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
return NULL;
}
static SymOpList *make_222()
{
+ SymOpList *new = new_symoplist();
+ add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* 2 */
+ add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
return NULL;
}
static SymOpList *make_mm2()
{
+ SymOpList *new = new_symoplist();
+ add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* 2 */
+ add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
return NULL;
}
@@ -222,6 +331,8 @@ static SymOpList *make_4m()
static SymOpList *make_4()
{
+ SymOpList *new = new_symoplist();
+ add_symop(new, v(0,1,0,0), v(1,0,0,0), v(0,0,0,1)); /* 4 */
return NULL;
}
@@ -305,8 +416,6 @@ static SymOpList *make_6mm()
/************************************ Cubic ***********************************/
-
-
SymOpList *get_pointgroup(const char *sym)
{
/* Triclinic */
@@ -340,18 +449,19 @@ SymOpList *get_pointgroup(const char *sym)
if ( strcmp(sym, "622") == 0 ) return make_622();
if ( strcmp(sym, "6bar2m") == 0 ) return make_6bar2m();
if ( strcmp(sym, "6mm") == 0 ) return make_6mm();
+
+ ERROR("Unknown point group '%s'\n", sym);
+ return NULL;
}
-/**
- * num_ops:
- * @ops: A %SymOpList
- *
- * Returns: the number of operations in @ops.
- **/
-int num_ops(SymOpList *ops)
+static void do_op(struct sym_op *op,
+ signed int h, signed int k, signed int l,
+ signed int *he, signed int *ke, signed int *le)
{
- return ops->n_ops;
+ *he = h*op->h[0] + k*op->h[1] + l*op->h[2];
+ *ke = h*op->k[0] + k*op->h[1] + l*op->k[2];
+ *le = h*op->l[0] + k*op->h[1] + l*op->l[2];
}
@@ -379,12 +489,32 @@ void get_equiv(SymOpList *ops, int idx,
signed int h, signed int k, signed int l,
signed int *he, signed int *ke, signed int *le)
{
- signed int i = -h-k;
- struct sym_op op = ops->ops[idx];
+ int sig[32];
+ int divisors[32];
+ int i, n, r;
- *he = h*op.h[0] + k*op.h[1] + i*op.h[2] + l*op.h[3];
- *ke = h*op.k[0] + k*op.h[1] + i*op.k[2] + l*op.k[3];
- *le = h*op.l[0] + k*op.h[1] + i*op.l[2] + l*op.l[3];
+ n = num_ops(ops);
+ divisors[0] = 1;
+ for ( i=1; i<n; i++ ) {
+ divisors[i] = divisors[i-1]*ops->ops[i].order;
+ }
+ r = idx;
+ for ( i=n-1; i>=0; i-- ) {
+ sig[i] = r / divisors[i];
+ r = r % divisors[i];
+ assert(sig[i] < ops->ops[i].order);
+ }
+
+ for ( i=0; i<n; i++ ) {
+
+ int s;
+
+ /* Do this operation "sig[i]" times */
+ for ( s=0; s<sig[i]; s++ ) {
+ do_op(&ops->ops[i], h, k, l, &h, &k, &l);
+ }
+
+ }
}
@@ -404,25 +534,23 @@ void get_equiv(SymOpList *ops, int idx,
SymOpList *special_position(SymOpList *ops,
signed int h, signed int k, signed int l)
{
- int n_general;
- int i;
- SymOpList *equivs;
- int n_equivs = 0;
+ int i, n;
+ SymOpList *specialised;
- equivs = new_symoplist();
+ n = num_ops(ops);
+ specialised = new_symoplist();
- for ( i=0; i<num_ops(ops); i++ ) {
+ for ( i=0; i<n; i++ ) {
signed int ht, kt, lt;
- /* Get equivalent according to the point group */
- get_equiv(ops, i, h, k, l, &ht, &kt, &lt);
-
- if (
+ do_op(&ops->ops[i], h, k, l, &ht, &kt, &lt);
+ if ( (h==ht) || (k==kt) || (l==lt) ) continue;
+ add_copied_symop(specialised, &ops->ops[i]);
}
- return equivs;
+ return specialised;
}
@@ -430,14 +558,14 @@ void get_asymm(SymOpList *ops, int idx,
signed int h, signed int k, signed int l,
signed int *hp, signed int *kp, signed int *lp)
{
- int nequiv = num_equivs(h, k, l, sym);
+ int nequiv = num_equivs(ops);
int p;
signed int best_h, best_k, best_l;
best_h = h; best_k = k; best_l = l;
for ( p=0; p<nequiv; p++ ) {
- get_equiv(h, k, l, hp, kp, lp, sym, p);
+ get_equiv(ops, p, h, k, l, hp, kp, lp);
if ( h > best_h ) {
best_h = h; best_k = k; best_l = l;
@@ -471,7 +599,6 @@ SymOpList *get_twins(SymOpList *source, SymOpList *target)
{
int n_src, n_tgt;
int i;
- signed int h, k, l;
SymOpList *twins = new_symoplist();
n_src = num_ops(source);