diff --git a/src/Configuration.cpp b/src/Configuration.cpp
index ecfbec92199fac87815148d26abb974c5c5e9085..16a57e973a15f2a224716c1c447acff18446c951 100644
--- a/src/Configuration.cpp
+++ b/src/Configuration.cpp
@@ -113,9 +113,14 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
}
}
+
+ /* Initialize exclusions */
+ excludeCapacity = 256;
+ numExcludes = 0;
+ excludes = new Exclude[excludeCapacity];
- if (readBondsFromFile) readBonds();
if (readExcludesFromFile) readExcludes();
+ if (readBondsFromFile) readBonds();
if (readAnglesFromFile) readAngles();
if (readDihedralsFromFile) readDihedrals();
if (readRestraintsFromFile) readRestraints();
@@ -281,35 +286,10 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
for (int i = oldNumExcludes; i < numExcludes; i++)
excludes[i] = newExcludes[i - oldNumExcludes];
printf("Built %d exclusions.\n",numExcludes);
-
- // Call compareExcludeIndex with qsort to sort the excludes by BOTH ind1 AND ind2
- std::sort(excludes, excludes + numExcludes, compare());
-
- /* Each particle may have a varying number of excludes
- * excludeMap is an array with one element for each particle
- * which keeps track of where a particle's excludes are stored
- * in the excludes array.
- * excludeMap[i].x is the index in the excludes array where the ith particle's excludes begin
- * 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++) {
- excludeMap[i].x = -1;
- excludeMap[i].y = -1;
- }
- int currPart = -1;
- int lastPart = -1;
- for (int i = 0; i < numExcludes; i++) {
- if (excludes[i].ind1 != currPart) {
- currPart = excludes[i].ind1;
- excludeMap[currPart].x = i;
- if (lastPart >= 0)
- excludeMap[lastPart].y = i;
- lastPart = currPart;
- }
- }
}
+ buildExcludeMap();
+
// Count number of particles of each type
numPartsOfType = new int[numParts];
for (int i = 0; i < numParts; ++i) {
@@ -1120,6 +1100,12 @@ void Configuration::readBonds() {
printf("WARNING: Invalid bond file line: %s\n", line);
continue;
}
+
+ if (ind1 < 0 || ind1 >= num || ind2 < 0 || ind2 >=num) {
+ printf("ERROR: Bond file line '%s' includes invalid index\n", line);
+ exit(1);
+ }
+
// If we don't have enough room in our bond array, we need to expand it.
if (numBonds+1 >= capacity) { // "numBonds+1" because we are adding two bonds to array
@@ -1143,17 +1129,9 @@ void Configuration::readBonds() {
// We must add it twice: Once for (ind1, ind2) and once for (ind2, ind1)
// RBTODO: add ind1/2 to exclusion list here iff op == REPLACE
- /*if (op == Bond::REPLACE)
- if( (int)(op) == 1)
- {
- printf("WARNING: Bond exclusions not implemented\n");
- continue;
- }*/
- if (ind1 < 0 || ind1 >= num || ind2 < 0 || ind2 >=num) {
- printf("ERROR: Bond file line '%s' includes invalid index\n", line);
- exit(1);
- }
+ if (op == "REPLACE")
+ addExclusion(ind1, ind2);
Bond* b = new Bond(op, ind1, ind2, file_name);
bonds[numBonds++] = *b;
@@ -1203,11 +1181,6 @@ void Configuration::readExcludes()
return;
}
- // Our particle array has a starting capacity of 256
- // We will expand this later if we need to.
- excludeCapacity = 256;
- numExcludes = 0;
- excludes = new Exclude[excludeCapacity];
// Get and process all lines of input
while (fgets(line, 256, inp) != NULL) {
@@ -1230,65 +1203,74 @@ void Configuration::readExcludes()
}
int ind1 = atoi(tokenList[1].val());
int ind2 = atoi(tokenList[2].val());
- if (ind1 >= num || ind2 >= num)
- continue;
+ addExclusion(ind1, ind2);
+ delete[] tokenList;
+ }
+}
+void Configuration::addExclusion(int ind1, int ind2) {
+ if (ind1 >= num || ind2 >= num) {
+ printf("WARNING: Attempted to add an exclusion for an out-of-range particle index (%d or %d >= %d).\n", ind1, ind2, num);
+ return;
+ }
- // If we don't have enough room in our bond array, we need to expand it.
- if (numExcludes >= excludeCapacity) {
- // Temporary pointer to the old array
- Exclude* temp = excludes;
+ // If we don't have enough room in our bond array, we need to expand it.
+ if (numExcludes >= excludeCapacity) {
+ // Temporary pointer to the old array
+ Exclude* temp = excludes;
- // Double the capacity
- excludeCapacity *= 2;
+ // Double the capacity
+ excludeCapacity *= 2;
- // Create pointer to new array which is twice the size of the old one
- excludes = new Exclude[excludeCapacity];
+ // Create pointer to new array which is twice the size of the old one
+ excludes = new Exclude[excludeCapacity];
- // Copy the old values into the new array
- for (int j = 0; j < numExcludes; j++)
- excludes[j] = temp[j];
+ // Copy the old values into the new array
+ for (int j = 0; j < numExcludes; j++)
+ excludes[j] = temp[j];
- // delete the old array
- delete[] temp;
- }
- // Add the bond to the exclude array
- // We must add it twice: Once for (ind1, ind2) and once for (ind2, ind1)
- Exclude ex(ind1, ind2);
- excludes[numExcludes++] = ex;
- Exclude ex2(ind2, ind1);
- excludes[numExcludes++] = ex2;
- delete[] tokenList;
- }
- // Call compareExcludeIndex with qsort to sort the excludes by BOTH ind1 AND ind2
- std::sort(excludes, excludes + numExcludes, compare());
-
- /* Each particle may have a varying number of excludes
- * excludeMap is an array with one element for each particle
- * which keeps track of where a particle's excludes are stored
- * in the excludes array.
- * excludeMap[i].x is the index in the excludes array where the ith particle's excludes begin
- * excludeMap[i].y is the index in the excludes array where the ith particle's excludes end
- */
- excludeMap = new int2[num];
- for (int i = 0; i < num; i++) {
- excludeMap[i].x = -1;
- excludeMap[i].y = -1;
- }
- int currPart = -1;
- int lastPart = -1;
- for (int i = 0; i < numExcludes; i++) {
- if (excludes[i].ind1 != currPart) {
- currPart = excludes[i].ind1;
- assert(currPart < num);
- excludeMap[currPart].x = i;
- if (lastPart >= 0)
- excludeMap[lastPart].y = i;
- lastPart = currPart;
- }
- }
- if (excludeMap[lastPart].x > 0)
- excludeMap[lastPart].y = numExcludes;
+ // delete the old array
+ delete[] temp;
+ }
+ // Add the bond to the exclude array
+ // We must add it twice: Once for (ind1, ind2) and once for (ind2, ind1)
+ Exclude ex1(ind1, ind2);
+ excludes[numExcludes++] = ex1;
+ Exclude ex2(ind2, ind1);
+ excludes[numExcludes++] = ex2;
+
+}
+
+void Configuration::buildExcludeMap() {
+ // Call compareExcludeIndex with qsort to sort the excludes by BOTH ind1 AND ind2
+ std::sort(excludes, excludes + numExcludes, compare());
+
+ /* Each particle may have a varying number of excludes
+ * excludeMap is an array with one element for each particle
+ * which keeps track of where a particle's excludes are stored
+ * in the excludes array.
+ * excludeMap[i].x is the index in the excludes array where the ith particle's excludes begin
+ * excludeMap[i].y is the index in the excludes array where the ith particle's excludes end
+ */
+ excludeMap = new int2[num];
+ for (int i = 0; i < num; i++) {
+ excludeMap[i].x = -1;
+ excludeMap[i].y = -1;
+ }
+ int currPart = -1;
+ int lastPart = -1;
+ for (int i = 0; i < numExcludes; i++) {
+ if (excludes[i].ind1 != currPart) {
+ currPart = excludes[i].ind1;
+ assert(currPart < num);
+ excludeMap[currPart].x = i;
+ if (lastPart >= 0)
+ excludeMap[lastPart].y = i;
+ lastPart = currPart;
+ }
+ }
+ if (excludeMap[lastPart].x > 0)
+ excludeMap[lastPart].y = numExcludes;
}
void Configuration::readAngles() {
diff --git a/src/Configuration.h b/src/Configuration.h
index d68168d46cbffc982b28fc2d8b17e0c8962175ad..4e8bad25420d95895f2b2a284af7c76db2368141 100644
--- a/src/Configuration.h
+++ b/src/Configuration.h
@@ -61,6 +61,8 @@ class Configuration {
void readAtoms();
void readBonds();
void readExcludes();
+ void addExclusion(int ind1, int ind2);
+ void buildExcludeMap();
void readDihedrals();
void readRestraints();