From add098ff6ce92430950ed094488c2bc5a239e215 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 7 Mar 2017 17:37:35 -0600
Subject: [PATCH] Added configuration options for specifying system size
---
src/Configuration.cpp | 44 +++++++++++++++++++++++++++++++++++--------
src/Configuration.h | 3 +++
2 files changed, 39 insertions(+), 8 deletions(-)
diff --git a/src/Configuration.cpp b/src/Configuration.cpp
index 7503560..ecfbec9 100644
--- a/src/Configuration.cpp
+++ b/src/Configuration.cpp
@@ -125,7 +125,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
printf("\nFound temperature grid file: %s\n", temperatureGridFile.val());
tGrid = new BaseGrid(temperatureGridFile.val());
printf("Loaded `%s'.\n", temperatureGridFile.val());
- printf("System size %s.\n", tGrid->getExtent().toString().val());
+ printf("Grid size %s.\n", tGrid->getExtent().toString().val());
// TODO: ask Max Belkin what this is about and how to remove hard-coded temps
float ToSo = 1.0f / (295.0f * 4.634248239f); // 1 / (To * sigma(To))
@@ -158,7 +158,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
part[i].meanPmf = part[i].pmf->mean();
printf("Loaded dx potential grid `%s'.\n", map.val());
- printf("System size %s.\n", part[i].pmf->getExtent().toString().val());
+ printf("Grid size %s.\n", part[i].pmf->getExtent().toString().val());
} else if (len >= 4 && map[len-4]=='.' && map[len-3]=='d' && map[len-2]=='e' && map[len-1]=='f') {
// A system definition file.
String rootGrid = OverlordGrid::readDefFirst(map);
@@ -178,25 +178,25 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
if (partForceXGridFile[i].length() != 0) {
part[i].forceXGrid = new BaseGrid(partForceXGridFile[i].val());
printf("Loaded `%s'.\n", partForceXGridFile[i].val());
- printf("System size %s.\n", part[i].forceXGrid->getExtent().toString().val());
+ printf("Grid size %s.\n", part[i].forceXGrid->getExtent().toString().val());
}
if (partForceYGridFile[i].length() != 0) {
part[i].forceYGrid = new BaseGrid(partForceYGridFile[i].val());
printf("Loaded `%s'.\n", partForceYGridFile[i].val());
- printf("System size %s.\n", part[i].forceYGrid->getExtent().toString().val());
+ printf("Grid size %s.\n", part[i].forceYGrid->getExtent().toString().val());
}
if (partForceZGridFile[i].length() != 0) {
part[i].forceZGrid = new BaseGrid(partForceZGridFile[i].val());
printf("Loaded `%s'.\n", partForceZGridFile[i].val());
- printf("System size %s.\n", part[i].forceZGrid->getExtent().toString().val());
+ printf("Grid size %s.\n", part[i].forceZGrid->getExtent().toString().val());
}
if (partDiffusionGridFile[i].length() != 0) {
part[i].diffusionGrid = new BaseGrid(partDiffusionGridFile[i].val());
printf("Loaded `%s'.\n", partDiffusionGridFile[i].val());
- printf("System size %s.\n", part[i].diffusionGrid->getExtent().toString().val());
+ printf("Grid size %s.\n", part[i].diffusionGrid->getExtent().toString().val());
}
if (temperatureGridFile.length() != 0) {
@@ -211,7 +211,6 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
// part[i].diffusionGrid->write(outFile, comment);
}
}
-
}
// Load reservoir files if any
@@ -226,8 +225,20 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
// Get the system dimensions
// from the dimensions of supplied 3D potential maps
+ if (size.length2() > 0) { // use size if it's defined
+ if (basis1.length2() > 0 || basis2.length2() > 0 || basis3.length2() > 0)
+ printf("WARNING: both 'size' and 'basis' were specified... using 'size'\n");
+ basis1 = Vector3(size.x,0,0);
+ basis2 = Vector3(0,size.y,0);
+ basis3 = Vector3(0,0,size.z);
+ }
+ if (basis1.length2() > 0 && basis2.length2() > 0 && basis3.length2() > 0) {
+ sys = new BaseGrid( Matrix3(basis1,basis2,basis3), origin, 1, 1, 1 );
+ } else {
+ // TODO: use largest system in x,y,z
sys = part[0].pmf;
- sysDim = part[0].pmf->getExtent();
+ }
+ sysDim = sys->getExtent();
// RBTODO: clean this mess up
/* // RigidBodies... */
@@ -541,6 +552,13 @@ void Configuration::setDefaults() {
rigidBodyGridGridPeriod = 1;
steps = 100;
seed = 0;
+
+ origin = Vector3(0,0,0);
+ size = Vector3(0,0,0);
+ basis1 = Vector3(0,0,0);
+ basis2 = Vector3(0,0,0);
+ basis3 = Vector3(0,0,0);
+
inputCoordinates = "";
restartCoordinates = "";
numberFluct = 0;
@@ -662,6 +680,16 @@ int Configuration::readParameters(const char * config_file) {
steps = atol(value.val());
else if (param == String("seed"))
seed = atoi(value.val());
+ else if (param == String("origin"))
+ origin = stringToVector3( value );
+ else if (param == String("systemSize"))
+ size = stringToVector3( value );
+ else if (param == String("basis1"))
+ basis1 = stringToVector3( value );
+ else if (param == String("basis2"))
+ basis2 = stringToVector3( value );
+ else if (param == String("basis3"))
+ basis3 = stringToVector3( value );
else if (param == String("inputCoordinates"))
inputCoordinates = value;
else if (param == String("restartCoordinates"))
diff --git a/src/Configuration.h b/src/Configuration.h
index 64f4acf..d68168d 100644
--- a/src/Configuration.h
+++ b/src/Configuration.h
@@ -87,6 +87,9 @@ public:
// Output variables
Vector3 sysDim;
BaseGrid* sys;
+ // temporary variables
+ Vector3 origin, size, basis1, basis2, basis3;
+
bool loadedCoordinates;
--
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