Configuration.cpp

			while (low <= high) {
				mid = (int)((high - low) / 2 + low);
				int curr = indices[mid];
				if (curr < key) {
					low = mid + 1;
				} else if (curr > key) {
					high = mid - 1;
				} else {
					// For now, particles with non-unique IDs are simply not added to the array
					// Other possible approaches which are not yet implemented:
					// 1: Keep track of these particles and assign them new IDs after you have
					//    already added all of the other particles. 	
					// 2: Get rid of ALL particles with that ID, even the ones that have already 
					//    been added.
					printf("WARNING: Non-unique ID found: %s\n", line);
					uniqueID = false;
					break;
				}
			}
			if (uniqueID) {
				// Add the particle to the end of the array, then sort it. 
				indices[numPartsFromFile] = key;
				partsFromFile[numPartsFromFile++] = line;
				std::sort(indices, indices + numPartsFromFile);
				std::sort(partsFromFile, partsFromFile + numPartsFromFile, compare());		
			}
		}
	}
}

void Configuration::readBonds() {
	// Open the file
	FILE* inp = fopen(bondFile.val(), "r");
	char line[256];

	// If the particle file cannot be found, exit the program
	if (inp == NULL) {
		printf("WARNING: Could not open `%s'.\n", bondFile.val());
		printf("         This simulation will not use particle bonds.\n");
		return;
	}

	// Our particle array has a starting capacity of 256
	// We will expand this later if we need to.
	int capacity = 256;
	numBonds = 0;
	bonds = new Bond[capacity];

	// Get and process all lines of input
	while (fgets(line, 256, inp) != NULL) {
		
		// Lines in the particle file that begin with # are comments
		if (line[0] == '#') continue;
		      
		String s(line);
		int numTokens = s.tokenCount();
		      
		// Break the line down into pieces (tokens) so we can process them individually
		String* tokenList = new String[numTokens];
		s.tokenize(tokenList);

		// Legitimate BOND input lines have 4 tokens: 
		// BOND | OPERATION_FLAG | INDEX1 | INDEX2 | FILENAME 
		// A line without exactly five tokens should be discarded.
		if (numTokens != 5) {
			printf("WARNING: Invalid bond file line: %s\n", line);
			continue;
		}

		String op = tokenList[1];
		int ind1 = atoi(tokenList[2].val());
		int ind2 = atoi(tokenList[3].val());
		String file_name = tokenList[4];

		if (ind1 == ind2) {
			printf("WARNING: Invalid bond file line: %s\n", line);
			continue;
		}
		
		// 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
			// Temporary pointer to the old array
			Bond* temp = bonds;	

			// Double the capacity
			capacity *= 2;

			// Create pointer to new array which is twice the size of the old one
			bonds = new Bond[capacity];
		
			// Copy the old values into the new array
			for (int j = 0; j < numBonds; j++)
				bonds[j] = temp[j];

			// delete the old array
			delete[] temp;
		}
		// Add the bond to the bond array
		// 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);
		}

		Bond* b = new Bond(op, ind1, ind2, file_name);
		bonds[numBonds++] = *b;
		b = new Bond(op, ind2, ind1, file_name);
		bonds[numBonds++] = *b;
		delete[] tokenList;
	}	
	// Call compareBondIndex with qsort to sort the bonds by BOTH ind1 AND ind2
	std::sort(bonds, bonds + numBonds, compare());

	/* Each particle may have a varying number of bonds
	 * bondMap is an array with one element for each particle
	 * which keeps track of where a particle's bonds are stored
	 * in the bonds array.
	 * bondMap[i].x is the index in the bonds array where the ith particle's bonds begin
	 * bondMap[i].y is the index in the bonds array where the ith particle's bonds end
	 */
	bondMap = new int2[num];
	for (int i = 0; i < num; i++) {	
		bondMap[i].x = -1;
		bondMap[i].y = -1;
	}
	int currPart = -1;
	int lastPart = -1;
	for (int i = 0; i < numBonds; i++) {
		if (bonds[i].ind1 != currPart) {
			currPart = bonds[i].ind1;
			bondMap[currPart].x = i;
			if (lastPart >= 0) bondMap[lastPart].y = i;
			lastPart = currPart;
		}
	}
	if (bondMap[lastPart].x > 0)
		bondMap[lastPart].y = numBonds;
}

void Configuration::readExcludes()
{
	// Open the file
	FILE* inp = fopen(excludeFile.val(), "r");
	char line[256];

	// If the exclusion file cannot be found, exit the program
	if (inp == NULL) {
		printf("WARNING: Could not open `%s'.\n", excludeFile.val());
		printf("This simulation will not use exclusions.\n");
		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) {
		// Lines in the particle file that begin with # are comments
		if (line[0] == '#') continue;
		      
		String s(line);
		int numTokens = s.tokenCount();
		      
		// Break the line down into pieces (tokens) so we can process them individually
		String* tokenList = new String[numTokens];
		s.tokenize(tokenList);

		// Legitimate EXCLUDE input lines have 3 tokens: 
		// BOND | INDEX1 | INDEX2
		// A line without exactly three tokens should be discarded.
		if (numTokens != 3) {
			printf("WARNING: Invalid exclude file line: %s\n", line);
			continue;
		}
		int ind1 = atoi(tokenList[1].val());
		int ind2 = atoi(tokenList[2].val());
		if (ind1 >= num || ind2 >= num) 
			continue;
		
		// 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;

			// 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];

			// 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;

}

void Configuration::readAngles() {
	FILE* inp = fopen(angleFile.val(), "r");
	char line[256];
	int capacity = 256;
	numAngles = 0;
	angles = new Angle[capacity];

	// If the angle file cannot be found, exit the program
	if (inp == NULL) {
		printf("WARNING: Could not open `%s'.\n", angleFile.val());
		printf("This simulation will not use angles.\n");
		return;
	}

	while(fgets(line, 256, inp)) {
		if (line[0] == '#') continue;
		String s(line);
		int numTokens = s.tokenCount();
		String* tokenList = new String[numTokens];
		s.tokenize(tokenList);
		
		// Legitimate ANGLE inputs have 5 tokens
		// ANGLE | INDEX1 | INDEX2 | INDEX3 | FILENAME
		// Any angle input line without exactly 5 tokens should be discarded
		if (numTokens != 5) {
			printf("WARNING: Invalid angle input line: %s\n", line);
			continue;
		}		
		
		// Discard any empty line
		if (tokenList == NULL) 
			continue;
		
		int ind1 = atoi(tokenList[1].val());
		int ind2 = atoi(tokenList[2].val());
		int ind3 = atoi(tokenList[3].val());
		String file_name = tokenList[4];
		//printf("file_name %s\n", file_name.val());
		if (ind1 >= num or ind2 >= num or ind3 >= num)
			continue;

		if (numAngles >= capacity) {
			Angle* temp = angles;
			capacity *= 2;
			angles = new Angle[capacity];
			for (int i = 0; i < numAngles; i++)
				angles[i] = temp[i];
			delete[] temp;
		}

		Angle a(ind1, ind2, ind3, file_name);
		angles[numAngles++] = a;
		delete[] tokenList;
	}
	std::sort(angles, angles + numAngles, compare());	

	// for(int i = 0; i < numAngles; i++)
	// 	angles[i].print();
}

void Configuration::readDihedrals() {
	FILE* inp = fopen(dihedralFile.val(), "r");
	char line[256];
	int capacity = 256;
	numDihedrals = 0;
	dihedrals = new Dihedral[capacity];

	// If the dihedral file cannot be found, exit the program
	if (inp == NULL) {
		printf("WARNING: Could not open `%s'.\n", dihedralFile.val());
		printf("This simulation will not use dihedrals.\n");
		return;
	}

	while(fgets(line, 256, inp)) {
		if (line[0] == '#') continue;
		String s(line);
		int numTokens = s.tokenCount();
		String* tokenList = new String[numTokens];
		s.tokenize(tokenList);
		
		// Legitimate DIHEDRAL inputs have 6 tokens
		// DIHEDRAL | INDEX1 | INDEX2 | INDEX3 | INDEX4 | FILENAME
		// Any angle input line without exactly 6 tokens should be discarded
		if (numTokens != 6) {
			printf("WARNING: Invalid dihedral input line: %s\n", line);
			continue;
		}		
		
		// Discard any empty line
		if (tokenList == NULL) 
			continue;
		
		int ind1 = atoi(tokenList[1].val());
		int ind2 = atoi(tokenList[2].val());
		int ind3 = atoi(tokenList[3].val());
		int ind4 = atoi(tokenList[4].val());
		String file_name = tokenList[5];
		//printf("file_name %s\n", file_name.val());
		if (ind1 >= num or ind2 >= num
				or ind3 >= num or ind4 >= num)
			continue;

		if (numDihedrals >= capacity) {
			Dihedral* temp = dihedrals;
			capacity *= 2;
			dihedrals = new Dihedral[capacity];
			for (int i = 0; i < numDihedrals; ++i)
				dihedrals[i] = temp[i];
			delete[] temp;
		}

		Dihedral d(ind1, ind2, ind3, ind4, file_name);
		dihedrals[numDihedrals++] = d;
		delete[] tokenList;
	}
	std::sort(dihedrals, dihedrals + numDihedrals, compare());	

	// for(int i = 0; i < numDihedrals; i++)
	// 	dihedrals[i].print();
}

void Configuration::populate() {
	int pn = 0;
	int p = 0;

	for (int i = 0; i < num; i++) {
		for (int s = 0; s < simNum; ++s)
			type[i + s*num] = p;
		serial[i] = currSerial++;
		if (++pn >= part[p].num) {
			p++;
			pn = 0;
		}
	}
}

bool Configuration::readBondFile(const String& value, int currBond) {
	int numTokens = value.tokenCount();
	if (numTokens != 1) {
		printf("ERROR: Invalid tabulatedBondFile: %s, numTokens = %d\n", value.val(), numTokens);
		return false;
	}

	String* tokenList = new String[numTokens];
	value.tokenize(tokenList);
	if (tokenList == NULL) {
		printf("ERROR: Invalid tabulatedBondFile: %s; tokenList is NULL\n", value.val());
		return false;
	}

	bondTableFile[currBond] = tokenList[0];

	// printf("Tabulated Bond Potential: %s\n", bondTableFile[currBond].val() );

	return true;
}

bool Configuration::readAngleFile(const String& value, int currAngle) {
	int numTokens = value.tokenCount();
	if (numTokens != 1) {
		printf("ERROR: Invalid tabulatedAngleFile: %s, numTokens = %d\n", value.val(), numTokens);
		return false;
	}

	String* tokenList = new String[numTokens];
	value.tokenize(tokenList);
	if (tokenList == NULL) {
		printf("ERROR: Invalid tabulatedAngleFile: %s; tokenList is NULL\n", value.val());
		return false;
	}

	angleTableFile[currAngle] = tokenList[0];

	// printf("Tabulated Angle Potential: %s\n", angleTableFile[currAngle].val() );

	return true;
}

bool Configuration::readDihedralFile(const String& value, int currDihedral) {
	int numTokens = value.tokenCount();
	if (numTokens != 1) {
		printf("ERROR: Invalid tabulatedDihedralFile: %s, numTokens = %d\n", value.val(), numTokens);
		return false;
	}

	String* tokenList = new String[numTokens];
	value.tokenize(tokenList);
	if (tokenList == NULL) {
		printf("ERROR: Invalid tabulatedDihedralFile: %s; tokenList is NULL\n", value.val());
		return false;
	}

	dihedralTableFile[currDihedral] = tokenList[0];

	// printf("Tabulated Dihedral Potential: %s\n", dihedralTableFile[currDihedral].val() );

	return true;
}

void Configuration::loadRestart(const char* file_name) {
	char line[STRLEN];
	FILE* inp = fopen(file_name, "r");

	if (inp == NULL) {
		printf("GrandBrownTown:loadRestart File `%s' does not exist\n", file_name);
		exit(-1);
	}

	int count = 0;
	while (fgets(line, STRLEN, inp) != NULL) {
		// Ignore comments.
		int len = strlen(line);
		if (line[0] == '#') continue;
		if (len < 2) continue;

		String s(line);
		int numTokens = s.tokenCount();
		if (numTokens != 4) {
			printf("GrandBrownTown:loadRestart Invalid coordinate file line: %s\n", line);
			fclose(inp);	
			exit(-1);
		}

		String* tokenList = new String[numTokens];
		s.tokenize(tokenList);
		if (tokenList == NULL) {
			printf("GrandBrownTown:loadRestart Invalid coordinate file line: %s\n", line);
			fclose(inp);
			exit(-1);
		}

		int typ = atoi(tokenList[0]);
		float x = (float) strtod(tokenList[1],NULL);
		float y = (float) strtod(tokenList[2],NULL);
		float z = (float) strtod(tokenList[3],NULL);

		pos[count] = Vector3(x,y,z);
		type[count] = typ;
		serial[count] = currSerial;
		currSerial++;
		if (typ < 0 || typ >= numParts) {
			printf("GrandBrownTown:countRestart Invalid particle type: %d\n", typ);
			fclose(inp);
			exit(-1);
		}

		count++;
		delete[] tokenList;
	}

	fclose(inp);    
}

bool Configuration::loadCoordinates(const char* file_name) {
	char line[STRLEN];
	FILE* inp = fopen(file_name, "r");

	if (inp == NULL) return false;

	int count = 0;
	while (fgets(line, STRLEN, inp) != NULL) {
		// Ignore comments.
		int len = strlen(line);
		if (line[0] == '#') continue;
		if (len < 2) continue;

		String s(line);
		int numTokens = s.tokenCount();
		if (numTokens != 3) {
			printf("ERROR: Invalid coordinate file line: %s\n", line);
			fclose(inp);	
			return false;
		}

		String* tokenList = new String[numTokens];
		s.tokenize(tokenList);
		if (tokenList == NULL) {
			printf("ERROR: Invalid coordinate file line: %s\n", line);
			fclose(inp);
			return false;
		}

		if (count >= num) {
			printf("WARNING: Too many coordinates in coordinate file %s.\n", file_name);
			fclose(inp);
			return true;
		}

		float x = (float) strtod(tokenList[0],NULL);
		float y = (float) strtod(tokenList[1],NULL);
		float z = (float) strtod(tokenList[2],NULL);
		pos[count] = Vector3(x,y,z);
		count++;

		delete[] tokenList;
	}
	fclose(inp);

	if (count < num) {
		printf("ERROR: Too few coordinates in coordinate file.\n");
		return false;
	}
	return true;
}

// Count the number of atoms in the restart file.
int Configuration::countRestart(const char* file_name) {
	char line[STRLEN];
	FILE* inp = fopen(file_name, "r");

	if (inp == NULL) {
		printf("ERROR: countRestart File `%s' does not exist\n", file_name);
		exit(-1);
	}

	int count = 0;
	while (fgets(line, STRLEN, inp) != NULL) {
		int len = strlen(line);
		// Ignore comments.
		if (line[0] == '#') continue;
		if (len < 2) continue;

		String s(line);
		int numTokens = s.tokenCount();
		if (numTokens != 4) {
			printf("ERROR: countRestart Invalid coordinate file line: %s\n", line);
			fclose(inp);	
			exit(-1);
		}

		String* tokenList = new String[numTokens];
		s.tokenize(tokenList);
		if (tokenList == NULL) {
			printf("ERROR: countRestart Invalid coordinate file line: %s\n", line);
			fclose(inp);
			exit(-1);
		}

		int typ = atoi(tokenList[0]);
		// float x = strtod(tokenList[1],NULL);
		// float y = strtod(tokenList[2],NULL);
		// float z = strtod(tokenList[3],NULL);
		if (typ < 0 || typ >= numParts) {
			printf("ERROR: countRestart Invalid particle type: %d\n", typ);
			fclose(inp);
			exit(-1);
		}

		count++;
		delete[] tokenList;
	}

	fclose(inp);    
	return count;
}

bool Configuration::readTableFile(const String& value, int currTab) {
	int numTokens = value.tokenCount('@');
	if (numTokens != 3) {
		printf("ERROR: Invalid tabulatedFile: %s\n", value.val());
		return false;
	}

	String* tokenList = new String[numTokens];
	value.tokenize(tokenList, '@');
	if (tokenList == NULL) {
		printf("ERROR: Invalid tabulatedFile: %s\n", value.val());
		return false;
	}

	partTableIndex0[currTab] = atoi(tokenList[0]);
	partTableIndex1[currTab] = atoi(tokenList[1]);
	partTableFile[currTab] = tokenList[2];

	// printf("Tabulated Potential: %d %d %s\n", partTableIndex0[currTab],
	// 		partTableIndex1[currTab], partTableFile[currTab].val() );
	delete[] tokenList;
	return true;
}

void Configuration::getDebugForce() {
	// Allow the user to choose which force computation to use
	printf("\n");
	printf("(1) ComputeFull [Default]          (2) ComputeSoftcoreFull\n");
	printf("(3) ComputeElecFull                (4) Compute (Decomposed)\n");
	printf("(5) ComputeTabulated (Decomposed)  (6) ComputeTabulatedFull\n");

	printf("WARNING: ");
	if (tabulatedPotential) {
		if (fullLongRange) printf("(6) was specified by config file\n");
		else printf("(5) was specified by config file\n");
	} else {
		if (fullLongRange != 0) printf("(%d) was specified by config file\n", fullLongRange);
		else printf("(4) was specified by config file\n");
	}

	char buffer[256];
	int choice;
	while (true) {
		printf("Choose a force computation (1 - 6): ");
		fgets(buffer, 256, stdin);
		bool good = sscanf(buffer, "%d", &choice) && (choice >= 1 && choice <= 6);
		if (good)
			break;
	}
	switch(choice) {
		case 1:
			tabulatedPotential = 0;
			fullLongRange = 1;
			break;
		case 2:
			tabulatedPotential = 0;
			fullLongRange = 2;
			break;
		case 3:
			tabulatedPotential = 0;
			fullLongRange = 3;
			break;
		case 4:
			tabulatedPotential = 0;
			fullLongRange = 0;
			break;
		case 5:
			tabulatedPotential = 1;
			fullLongRange = 0;
			break;
		case 6:
			tabulatedPotential = 1;
			fullLongRange = 1;
			break;
		default:
			tabulatedPotential = 0;
			fullLongRange = 1;
			break;
	}
	printf("\n");
}

//////////////////////////
// Comparison operators //
//////////////////////////
bool Configuration::compare::operator()(const String& lhs, const String& rhs) {
	String* list_lhs = new String[lhs.tokenCount()];
	String* list_rhs = new String[rhs.tokenCount()];
	lhs.tokenize(list_lhs);
	rhs.tokenize(list_rhs);
	int key_lhs = atoi(list_lhs[1].val());
	int key_rhs = atoi(list_rhs[1].val());
	delete[] list_lhs;
	delete[] list_rhs;
	return key_lhs < key_rhs;
}

bool Configuration::compare::operator()(const Bond& lhs, const Bond& rhs) {
	int diff = lhs.ind1 - rhs.ind1;
	if (diff != 0)
		return lhs.ind1 < rhs.ind1;
	return lhs.ind2 < rhs.ind2;
}

bool Configuration::compare::operator()(const Exclude& lhs, const Exclude& rhs) {
	int diff = lhs.ind1 - rhs.ind1;
	if (diff != 0)
		return lhs.ind1 < rhs.ind1;
	return lhs.ind2 < rhs.ind2;
}

bool Configuration::compare::operator()(const Angle& lhs, const Angle& rhs) {
	int diff = lhs.ind1 - rhs.ind1;
	if (diff != 0)
		return lhs.ind1 < rhs.ind1;
	diff = lhs.ind2 - rhs.ind2;
	if (diff != 0)
		return lhs.ind2 < rhs.ind2;
	return lhs.ind3 < rhs.ind3;
}

bool Configuration::compare::operator()(const Dihedral& lhs, const Dihedral& rhs) {
	int diff = lhs.ind1 - rhs.ind1;
	if (diff != 0) 
		return lhs.ind1 < rhs.ind1;
	diff = lhs.ind2 - rhs.ind2;
	if (diff != 0) 
		return lhs.ind2 < rhs.ind2;
	diff = lhs.ind3 - rhs.ind3;
	if (diff != 0) 
		return lhs.ind3 < rhs.ind3;
	return lhs.ind4 < rhs.ind4;
}