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authorThomas White <taw@bitwiz.org.uk>2010-11-28 22:21:19 +0100
committerThomas White <taw@physics.org>2012-02-22 15:27:07 +0100
commitaf89b9191e7d5b4f1b4111841550bba57f949902 (patch)
treec62817da5f60376e69541e7defabdcac72aaf9b1
parent3f4a70dccc16fd5aeb1b327b2b5040ac25b33c48 (diff)
pattern_sim: Add --min-size and --max-size options
-rw-r--r--src/pattern_sim.c61
1 files changed, 55 insertions, 6 deletions
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 75755020..d32f0ae8 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -85,6 +85,11 @@ static void show_help(const char *s)
" --really-random Use really random numbers for the orientation and\n"
" crystal size. By default, the same sequence\n"
" will be used for each new run.\n"
+" --min-size=<s> Generate random crystal sizes using <s> as the\n"
+" minimum crystal size in nm. --max-size is also\n"
+" required.\n"
+" --max-size=<s> Use <s> as the maximum crystal size in nm.\n"
+" --min-size is also required.\n"
"\n"
"By default, the simulation aims to be as accurate as possible. For greater\n"
"speed, or for testing, you can choose to disable certain things using the\n"
@@ -174,6 +179,18 @@ static struct quaternion read_quaternion()
}
+static int random_ncells(double len, double min_nm, double max_nm)
+{
+ int min_cells, max_cells, wid;
+
+ min_cells = min_nm*1e-9 / len;
+ max_cells = max_nm*1e-9 / len;
+ wid = max_cells - min_cells;
+
+ return wid*random()/RAND_MAX + min_cells;
+}
+
+
int main(int argc, char *argv[])
{
int c;
@@ -206,6 +223,9 @@ int main(int argc, char *argv[])
UnitCell *input_cell;
struct quaternion orientation;
int gpu_dev = -1;
+ int random_size = 0;
+ double min_size = 0.0;
+ double max_size = 0.0;
/* Long options */
const struct option longopts[] = {
@@ -227,6 +247,8 @@ int main(int argc, char *argv[])
{"beam", 1, NULL, 'b'},
{"really-random", 0, &config_random, 1},
{"gpu-dev", 1, NULL, 2},
+ {"min-size", 1, NULL, 3},
+ {"max-size", 1, NULL, 4},
{0, 0, NULL, 0}
};
@@ -279,6 +301,16 @@ int main(int argc, char *argv[])
gpu_dev = atoi(optarg);
break;
+ case 3 :
+ min_size = atof(optarg);
+ random_size++;
+ break;
+
+ case 4 :
+ max_size = atof(optarg);
+ random_size++;
+ break;
+
case 0 :
break;
@@ -297,6 +329,11 @@ int main(int argc, char *argv[])
srand(seed);
}
+ if ( random_size == 1 ) {
+ ERROR("You must specify both --min-size and --max-size.\n");
+ return 1;
+ }
+
if ( filename == NULL ) {
filename = strdup("molecule.pdb");
}
@@ -418,12 +455,24 @@ int main(int argc, char *argv[])
double a, b, c, d;
UnitCell *cell;
- //na = 8*random()/RAND_MAX + 4;
- //nb = 8*random()/RAND_MAX + 4;
- //nc = 16*random()/RAND_MAX + 30;
- na = 24;
- nb = 24;
- nc = 40;
+ if ( random_size ) {
+
+ double alen, blen, clen, dis;
+
+ cell_get_parameters(input_cell, &alen, &blen, &clen,
+ &dis, &dis, &dis);
+
+ na = random_ncells(alen, min_size, max_size);
+ nb = random_ncells(blen, min_size, max_size);
+ nc = random_ncells(clen, min_size, max_size);
+
+ } else {
+
+ na = 8;
+ nb = 8;
+ nc = 8;
+
+ }
/* Read quaternion from stdin */
if ( config_randomquat ) {