schiff

commit 4a0eadada0928281eb8a9bcb5d47037f8ecc9c8f
parent ae06330ea8bbb88d6ac48d94eba4df92f96cc1b9
Author: Vincent Forest <vincent.forest@meso-star.com>
Date:   Tue, 22 Mar 2016 16:35:22 +0100

Rename the zeta lognormal attribute in mu

Diffstat:
M
doc/schiff-geometry.5
 | 
14
+++++++-------
M
src/schiff_args.c
 | 
10
+++++-----
M
src/schiff_geometry.c
 | 
2
+-
M
src/schiff_geometry.h
 | 
2
+-
M
src/test_schiff_cylinder.sh
 | 
2
+-
M
src/test_schiff_sphere.sh
 | 
6
+++---

6 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/doc/schiff-geometry.5 b/doc/schiff-geometry.5
@@ -60,10 +60,10 @@ aforementioned cumulative before linearly interpolating its bounds with respect
 to "r";
 .IP \(bu 4
 with the \fBlognormal\fR distribution, the parameter is distributed with respect
-to a mean value \fBzeta\fR and a standard deviation \fBsigma\fR as follow:
+to a mean value \fBmu\fR and a standard deviation \fBsigma\fR as follow:
 .IP " " 8
 P(x) dx = 1/(log(\fBsigma\fR)*x*sqrt(2*PI) *
-          exp(-(ln(x)-log(\fBzeta\fR))^2 / (2*log(\fBsigma\fR)^2)) dx
+          exp(-(ln(x)-log(\fBmu\fR))^2 / (2*log(\fBsigma\fR)^2)) dx
 .SS Grammar
 This section describes the \fBschiff\-geometry\fR grammar based on the YAML
 human readable data format [1]. The YAML format provides several ways to define
@@ -118,7 +118,7 @@ the example section for illustrations of such alternatives.
 .TP
 <\fIlognormal\fR> ::=
   \fBlognormal:
-    zeta: \fIREAL\fB
+    mu: \fIREAL\fB
     sigma: \fIREAL\fB
 .TP
 <\fIhistogram\fR> ::=
@@ -156,7 +156,7 @@ distributed with respect to a lognormal distribution:
   c:
     lognormal:
       sigma: 0.2
-      zeta: 1.3\fR
+      mu: 1.3\fR
 .PP
 Soft particles are ellipsoids whose aspect ratio of its semi\-principal axis is
 fixed. Its volume is equal to the volume of an equivalent sphere whose radius
@@ -177,7 +177,7 @@ discretized in 64 slices along 2PI:
 \fBcylinder:
   slices: 64
   radius: 1
-  height: { lognormal: { zeta: 1.3, sigma: 0.84 } }\fR
+  height: { lognormal: { mu: 1.3, sigma: 0.84 } }\fR
 .PP
 Soft particles are cylinders whose height/radius ratio is fixed. Their volume
 is equal to the volume of a sphere whose radius is distributed with respect to
@@ -198,8 +198,8 @@ and spherical soft particles have a fixed radius:
 \fB- sphere: { radius 1.12, proba: 2.0, slices: 64 }
 .IP " " 4
 \fB- cylinder:
-  radius: {lognormal: { sigma: 2.3, zeta: 0.2 } }
-  height: {lognormal: { zeta: 1, sigma: 1.5 } }
+  radius: {lognormal: { sigma: 2.3, mu: 0.2 } }
+  height: {lognormal: { mu: 1, sigma: 1.5 } }
   slices: 32 # Discretisation in 32 slices
   proba: 1\fR
 .SH NOTE
diff --git a/src/schiff_args.c b/src/schiff_args.c
@@ -276,16 +276,16 @@ parse_yaml_param_lognormal
     val=yaml_document_get_node(doc, lognormal->data.mapping.pairs.start[i].value);
     ASSERT(key->type == YAML_SCALAR_NODE);
 
-    /* lognormal zeta attribute */
-    if(!strcmp((char*)key->data.scalar.value, "zeta")) {
+    /* lognormal mu attribute */
+    if(!strcmp((char*)key->data.scalar.value, "mu")) {
       if(mask & ZETA) {
         log_err(filename, key,
-          "the `zeta' lognormal attribute is already defined.\n");
+          "the `mu' lognormal attribute is already defined.\n");
         return RES_BAD_ARG;
       }
       mask |= ZETA;
       res = parse_yaml_double /* mean value */
-        (filename, val, min_val, max_val, &param->data.lognormal.zeta);
+        (filename, val, min_val, max_val, &param->data.lognormal.mu);
 
     /* lognormal sigma attribute */
     } else if(!strcmp((char*)key->data.scalar.value, "sigma")) {
@@ -309,7 +309,7 @@ parse_yaml_param_lognormal
 
   /* Ensure that the lognormal attributes are all parsed */
   if(!(mask & ZETA)) {
-    log_err(filename, lognormal, "missing the zeta lognormal attribute.\n");
+    log_err(filename, lognormal, "missing the mu lognormal attribute.\n");
     return RES_BAD_ARG;
   } else if(!(mask & SIGMA)) {
     log_err(filename, lognormal, "missing the sigma lognormal attribute.\n");
diff --git a/src/schiff_geometry.c b/src/schiff_geometry.c
@@ -139,7 +139,7 @@ eval_param(const struct schiff_param* param, struct ssp_rng* rng)
       val = param->data.constant;
       break;
     case SCHIFF_PARAM_LOGNORMAL:
-      val = ssp_ran_lognormal(rng, log(param->data.lognormal.zeta),
+      val = ssp_ran_lognormal(rng, log(param->data.lognormal.mu),
         log(param->data.lognormal.sigma));
       break;
     case SCHIFF_PARAM_HISTOGRAM:
diff --git a/src/schiff_geometry.h b/src/schiff_geometry.h
@@ -30,7 +30,7 @@ struct schiff_param {
   enum schiff_param_distribution distribution;
   union {
     double constant;
-    struct { double zeta, sigma; } lognormal;
+    struct { double mu, sigma; } lognormal;
     struct { double *entries, lower, upper; } histogram;
   } data;
 };
diff --git a/src/test_schiff_cylinder.sh b/src/test_schiff_cylinder.sh
@@ -370,7 +370,7 @@ then
     echo -e \
       "cylinder:\n" \
       "  aspect_ratio: $R\n" \
-      "  radius: { lognormal: { sigma: $sigma, zeta: $mean_radius } }\n" \
+      "  radius: { lognormal: { sigma: $sigma, mu: $mean_radius } }\n" \
       > $tmppipe &
 
     # Invoke the schiff command
diff --git a/src/test_schiff_sphere.sh b/src/test_schiff_sphere.sh
@@ -59,19 +59,19 @@ if [ ! -e $tmppipe ]; then mkfifo $tmppipe; fi
 
 if [ ! -f $tmpfile ]
 then
-  for zeta in ${mean_radius[*]}
+  for mu in ${mean_radius[*]}
   do
     # Generate the geometry distribution into the pipe
     echo -e \
       "sphere:\n" \
-      "  radius: { lognormal: { zeta: $zeta, sigma: $sigma } }" \
+      "  radius: { lognormal: { mu: $mu, sigma: $sigma } }" \
       > $tmppipe &
 
     # invoke the schiff command
     echo $wavelength $Nr $Kr $Ne | \
     schiff -q \
       -A $nangles \
-      -l $zeta \
+      -l $mu \
       -i $tmppipe \
       -w $wavelength \
       -g $nrealisations \