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authorThomas White <taw@physics.org>2013-08-09 18:00:58 +0200
committerThomas White <taw@physics.org>2013-09-13 14:35:01 +0200
commit9f5477e8e67748543ba7cf8131b1d1d41d616ee8 (patch)
tree6b3a751391ea93802408f2de764170dd7b8948ee
parent620d8f4c8a9e1805594a9240550f383b27368543 (diff)
Monoclinic changes for MOSFLM
-rw-r--r--libcrystfel/src/mosflm.c38
1 files changed, 31 insertions, 7 deletions
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index c9fcc125..fbd14e37 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -151,12 +151,13 @@ static int check_cell(struct mosflm_private *mp, struct image *image,
return 0;
}
- if ( cen_r != cen_m ) {
+ if ( (latt_m != L_MONOCLINIC) && (cen_r != cen_m) ) {
ERROR("Centering produced by MOSFLM (%c) does not "
"match what was requested (%c). "
"Please report this.\n", cen_m, cen_r);
return 0;
}
+ /* If it's monoclinic, see the warning in mosflm_prepare() */
}
@@ -214,28 +215,40 @@ static void mosflm_parseline(const char *line, struct image *image,
}
-/* This is the opposite of spacegroup_for_lattice() below. */
-static LatticeType spacegroup_to_lattice(const char *sg)
+/* This is the opposite of spacegroup_for_lattice() below.
+ * Note that this is not general, just a set of rules for interpreting MOSFLM's
+ * output. */
+static LatticeType spacegroup_to_lattice(const char *sg, char *ua, char *cen)
{
LatticeType latt;
+ *cen = sg[0];
+
if ( sg[1] == '1' ) {
latt = L_TRICLINIC;
+ *ua = '*';
} else if ( strncmp(sg+1, "23", 2) == 0 ) {
latt = L_CUBIC;
+ *ua = '*';
} else if ( strncmp(sg+1, "222", 3) == 0 ) {
latt = L_ORTHORHOMBIC;
+ *ua = '*';
} else if ( sg[1] == '2' ) {
latt = L_MONOCLINIC;
+ *ua = 'b';
} else if ( sg[1] == '4' ) {
latt = L_TETRAGONAL;
+ *ua = 'c';
} else if ( sg[1] == '6' ) {
latt = L_HEXAGONAL;
+ *ua = 'c';
} else if ( sg[1] == '3' ) {
if ( sg[0] == 'H' ) {
latt = L_HEXAGONAL;
+ *ua = 'c';
} else {
latt = L_RHOMBOHEDRAL;
+ *ua = '*';
}
} else {
ERROR("Couldn't understand '%s'\n", sg);
@@ -246,7 +259,6 @@ static LatticeType spacegroup_to_lattice(const char *sg)
}
-
static int read_newmat(struct mosflm_data *mosflm, const char *filename,
struct image *image)
{
@@ -262,6 +274,7 @@ static int read_newmat(struct mosflm_data *mosflm, const char *filename,
int i;
char cen;
LatticeType latt;
+ char ua = '?';
fh = fopen(filename, "r");
if ( fh == NULL ) {
@@ -293,12 +306,13 @@ static int read_newmat(struct mosflm_data *mosflm, const char *filename,
fclose(fh);
+ chomp(symm);
if ( strncmp(symm, "SYMM ", 5) != 0 ) {
ERROR("Bad 'SYMM' line from MOSFLM.\n");
return 1;
}
- cen = symm[5];
- latt = spacegroup_to_lattice(symm+5);
+ //STATUS("MOSFLM says '%s'\n", symm);
+ latt = spacegroup_to_lattice(symm+5, &ua, &cen);
/* MOSFLM "A" matrix is multiplied by lambda, so fix this */
c = 1.0/image->lambda;
@@ -315,6 +329,9 @@ static int read_newmat(struct mosflm_data *mosflm, const char *filename,
-csy*c, -csz*c, csx*c);
cell_set_centering(cell, cen);
cell_set_lattice_type(cell, latt);
+ cell_set_unique_axis(cell, ua);
+ //STATUS("My cell:\n");
+ //cell_print(cell);
if ( check_cell(mosflm->mp, image, cell) ) {
mosflm->success = 1;
@@ -444,9 +461,11 @@ static char *spacegroup_for_lattice(UnitCell *cell)
char centering;
char *g = NULL;
char *result;
+ char ua;
latt = cell_get_lattice_type(cell);
centering = cell_get_centering(cell);
+ ua = cell_get_unique_axis(cell);
switch ( latt )
{
@@ -455,7 +474,11 @@ static char *spacegroup_for_lattice(UnitCell *cell)
break;
case L_MONOCLINIC :
- g = "2";
+ switch ( ua ) {
+ case 'a' : g = "211"; break;
+ case 'b' : g = "121"; break;
+ case 'c' : g = "112"; break;
+ }
break;
case L_ORTHORHOMBIC :
@@ -519,6 +542,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
symm = spacegroup_for_lattice(mosflm->mp->template);
snprintf(tmp, 255, "SYMM %s\n", symm);
+ //STATUS("Asking MOSFLM for '%s'\n", symm);
free(symm);
mosflm_sendline(tmp, mosflm);