From ccc6ad02c6b8d617822f675bb7a041cdc496704c Mon Sep 17 00:00:00 2001
From: Maxim Belkin <maxim.belkin@gmail.com>
Date: Tue, 19 Jul 2016 14:42:00 -0500
Subject: [PATCH] Configuration.cpp: first attempt to reorganize the way
coordinates are read in
---
Configuration.cpp | 171 ++++++++++++++++++++++++----------------------
1 file changed, 88 insertions(+), 83 deletions(-)
diff --git a/Configuration.cpp b/Configuration.cpp
index 68b5db6..9332a16 100644
--- a/Configuration.cpp
+++ b/Configuration.cpp
@@ -22,34 +22,92 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
//dihedrals_d = NULL;
setDefaults();
readParameters(config_file);
- if (readPartsFromFile) readAtoms();
- // Get the initial number of particles.
- //
+ // Get the number of particles
printf("\nCounting particles specified in the ");
if (restartCoordinates.length() > 0) {
- // Read them from the restart file.
+ // Read them from the restart file.
printf("restart file.\n");
num = countRestart(restartCoordinates.val());
- } else if (numPartsFromFile == 0) {
- // Sum up all particles in config file
- printf("configuration file.\n");
- //int num0 = 0;
- num = 0;
- for (int i = 0; i < numParts; i++) num += part[i].num;
- //num = num0;
- } else {
- // Determine number of particles from input file (PDB-style)
- printf("input file.\n");
- num = numPartsFromFile;
- }
+ } else {
+ if (readPartsFromFile) readAtoms();
+ if (numPartsFromFile > 0) {
+ // Determine number of particles from input file (PDB-style)
+ printf("input file.\n");
+ num = numPartsFromFile;
+ } else {
+ // Sum up all particles in config file
+ printf("configuration file.\n");
+ //int num0 = 0;
+ num = 0;
+ for (int i = 0; i < numParts; i++) num += part[i].num;
+ //num = num0;
+ }
+ } // end result: variable "num" is set
- // Set the number capacity.
- printf("\n");
- printf("Initial particles: %d\n", num);
+
+ // Set the number capacity
+ printf("\nInitial particles: %d\n", num);
if (numCap <= 0) numCap = numCapFactor*num; // max number of particles
if (numCap <= 0) numCap = 20;
+ // Allocate particle variables.
+ pos = new Vector3[num * simNum];
+ type = new int[num * simNum];
+ serial = new int[num * simNum];
+ posLast = new Vector3[num * simNum];
+ name = new String[num * simNum];
+ currSerial = 0;
+
+
+ // Now, load the coordinates
+ loadedCoordinates = false;
+
+ // If we have a restart file - use it
+ if (restartCoordinates.length() > 0) {
+ loadRestart(restartCoordinates.val());
+ printf("Loaded %d restart coordinates from `%s'.\n", num, restartCoordinates.val());
+ printf("Particle numbers specified in the configuration file will be ignored.\n");
+ loadedCoordinates = true;
+ } else {
+ // Load coordinates from a file?
+ if (numPartsFromFile > 0) {
+ loadedCoordinates = true;
+ for (int i = 0; i < num; i++) {
+ int numTokens = partsFromFile[i].tokenCount();
+
+ // Break the line down into pieces (tokens) so we can process them individually
+ String* tokenList = new String[numTokens];
+ partsFromFile[i].tokenize(tokenList);
+
+ int currType = 0;
+ for (int j = 0; j < numParts; j++)
+ if (tokenList[2] == part[j].name)
+ currType = j;
+
+ for (int s = 0; s < simNum; ++s)
+ type[i + s*num] = currType;
+
+ serial[i] = currSerial++;
+
+ pos[i] = Vector3(atof(tokenList[3].val()),
+ atof(tokenList[4].val()),
+ atof(tokenList[5].val()));
+ }
+ delete[] partsFromFile;
+ partsFromFile = NULL;
+ } else {
+ // Not loading coordinates from a file
+ populate();
+ if (inputCoordinates.length() > 0) {
+ printf("Loading coordinates from %s ... ", inputCoordinates.val());
+ loadedCoordinates = loadCoordinates(inputCoordinates.val());
+ if (loadedCoordinates)
+ printf("done!\n");
+ }
+ }
+ }
+
if (readBondsFromFile) readBonds();
if (readExcludesFromFile) readExcludes();
@@ -69,7 +127,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
printf("Loaded `%s'.\n", temperatureGrid.val());
printf("System size %s.\n", tGrid->getExtent().toString().val());
- float ToSo = 1.0f / (295.0f * 4.634248239f); // 1 / (To * sigma(To))
+ float ToSo = 1.0f / (295.0f * 4.634248239f); // 1 / (To * sigma(To))
sigmaT = new BaseGrid(temperatureGrid.val());
sigmaT->shift(-122.8305f);
sigmaT->scale(0.0269167f);
@@ -123,7 +181,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
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());
- }
+ }
if (partForceZGridFile[i].length() != 0) {
part[i].forceZGrid = new BaseGrid(partForceZGridFile[i].val());
@@ -167,14 +225,6 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
sys = part[0].pmf;
sysDim = part[0].pmf->getExtent();
- // Allocate particle variables.
- pos = new Vector3[num * simNum];
- type = new int[num * simNum];
- serial = new int[num * simNum];
- posLast = new Vector3[num * simNum];
- name = new String[num * simNum];
- currSerial = 0;
-
// RBTODO: clean this mess up
/* // RigidBodies... */
/* if (numRigidTypes > 0) { */
@@ -195,24 +245,24 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
// // state data
// rbPos = new Vector3[numRB * simNum];
// type = new int[numRB * simNum];
-
+
/* } */
/* printf("Initial RigidBodies: %d\n", numRB); */
-
+
// Create exclusions from the exclude rule, if it was specified in the config file
if (excludeRule != String("")) {
int oldNumExcludes = numExcludes;
Exclude* newExcludes = makeExcludes(bonds, bondMap, num, numBonds, excludeRule, numExcludes);
if (excludes == NULL) {
- excludes = new Exclude[numExcludes];
- } else if (numExcludes >= excludeCapacity) {
+ excludes = new Exclude[numExcludes];
+ } else if (numExcludes >= excludeCapacity) {
Exclude* tempExcludes = excludes;
excludes = new Exclude[numExcludes];
for (int i = 0; i < oldNumExcludes; i++)
excludes[i] = tempExcludes[i];
delete tempExcludes;
- }
+ }
for (int i = oldNumExcludes; i < numExcludes; i++)
excludes[i] = newExcludes[i - oldNumExcludes];
printf("Built %d exclusions.\n",numExcludes);
@@ -228,7 +278,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
* excludeMap[i].y is the index in the excludes array where the ith particle's excludes end
*/
excludeMap = new int2[numPartsFromFile];
- for (int i = 0; i < numPartsFromFile; i++) {
+ for (int i = 0; i < numPartsFromFile; i++) {
excludeMap[i].x = -1;
excludeMap[i].y = -1;
}
@@ -254,7 +304,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
// inputCoordinates are ignored if restartCoordinates exist.
/*
if (restartCoordinates.length() > 0) {
- loadRestart(restartCoordinates.val());
+ loadRestart(restartCoordinates.val());
printf("Loaded %d restart coordinates from `%s'.\n", num, restartCoordinates.val());
printf("Particle numbers specified in the configuration file will be ignored.\n");
} else {
@@ -262,9 +312,9 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
// Load coordinates from a file?
if (numPartsFromFile > 0) {
- for (int i = 0; i < num; i++) {
+ for (int i = 0; i < num; i++) {
int numTokens = partsFromFile[i].tokenCount();
-
+
// Break the line down into pieces (tokens) so we can process them individually
String* tokenList = new String[numTokens];
partsFromFile[i].tokenize(tokenList);
@@ -292,52 +342,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
}
*/
- loadedCoordinates = false;
- // If we have a restart file - use it
- if (restartCoordinates.length() > 0) {
- loadRestart(restartCoordinates.val());
- printf("Loaded %d restart coordinates from `%s'.\n", num, restartCoordinates.val());
- printf("Particle numbers specified in the configuration file will be ignored.\n");
- loadedCoordinates = true;
- } else {
- // Load coordinates from a file?
- if (numPartsFromFile > 0) {
- loadedCoordinates = true;
- for (int i = 0; i < num; i++) {
- int numTokens = partsFromFile[i].tokenCount();
-
- // Break the line down into pieces (tokens) so we can process them individually
- String* tokenList = new String[numTokens];
- partsFromFile[i].tokenize(tokenList);
-
- int currType = 0;
- for (int j = 0; j < numParts; j++)
- if (tokenList[2] == part[j].name)
- currType = j;
-
- for (int s = 0; s < simNum; ++s)
- type[i + s*num] = currType;
-
- serial[i] = currSerial++;
-
- pos[i] = Vector3(atof(tokenList[3].val()),
- atof(tokenList[4].val()),
- atof(tokenList[5].val()));
- }
- delete[] partsFromFile;
- partsFromFile = NULL;
- } else {
- // Not loading coordinates from a file
- populate();
- if (inputCoordinates.length() > 0) {
- printf("Loading coordinates from %s ... ", inputCoordinates.val());
- loadedCoordinates = loadCoordinates(inputCoordinates.val());
- if (loadedCoordinates)
- printf("done!\n");
- }
- }
- }
// Get the maximum particle radius.
minimumSep = 0.0f;
for (int i = 0; i < numParts; ++i)
--
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