From 22c02ee016aa8655cb96fa6ac01fb63b9a2d5f9c Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 16 Apr 2021 19:14:50 -0500
Subject: [PATCH] Add restartRBCoordinates keyword and .rigid file reader
---
src/Configuration.cpp | 2 +
src/Configuration.h | 1 +
src/RigidBody.cu | 4 +-
src/RigidBodyController.cu | 97 +++++++++++++++++++++++++++++++++-----
src/RigidBodyController.h | 1 +
5 files changed, 90 insertions(+), 15 deletions(-)
diff --git a/src/Configuration.cpp b/src/Configuration.cpp
index ce8f153..b1a89c4 100644
--- a/src/Configuration.cpp
+++ b/src/Configuration.cpp
@@ -1137,6 +1137,8 @@ int Configuration::readParameters(const char * config_file) {
rigidBody[currRB].initAngularMomentum = stringToVector3(value);
else if (param == String("inputRBCoordinates"))
inputRBCoordinates = value;
+ else if (param == String("restartRBCoordinates"))
+ restartRBCoordinates = value;
// COMMON
else if (param == String("num")) {
diff --git a/src/Configuration.h b/src/Configuration.h
index 9daf4fe..fc70e2a 100644
--- a/src/Configuration.h
+++ b/src/Configuration.h
@@ -149,6 +149,7 @@ public:
String inputCoordinates;
String inputMomentum; //Han-Yi Chou
String inputRBCoordinates;
+ String restartRBCoordinates;
int copyReplicaCoordinates;
String restartCoordinates;
String restartMomentum; //Han-Yi Chou
diff --git a/src/RigidBody.cu b/src/RigidBody.cu
index 94e7261..e224d3d 100644
--- a/src/RigidBody.cu
+++ b/src/RigidBody.cu
@@ -69,8 +69,8 @@ void RigidBody::Boltzmann(unsigned long int seed)
angularMomentum.x *= sigma[1];
angularMomentum.y *= sigma[2];
angularMomentum.z *= sigma[3];
- printf("%f\n", Temp);
- printf("%f\n", Temperature());
+ // printf("%f\n", Temp);
+ // printf("%f\n", Temperature());
}
RigidBody::~RigidBody() {
diff --git a/src/RigidBodyController.cu b/src/RigidBodyController.cu
index 5c89ba2..c5e855e 100644
--- a/src/RigidBodyController.cu
+++ b/src/RigidBodyController.cu
@@ -80,24 +80,16 @@ RigidBodyController::RigidBodyController(const Configuration& c, const char* pre
gpuErrchk(cudaMallocHost(&(particleForces), sizeof(ForceEnergy) * 2*totalParticleForceNumBlocks))
gpuErrchk(cudaMalloc(&(particleForces_d), sizeof(ForceEnergy) * 2*totalParticleForceNumBlocks))
- if (conf.inputRBCoordinates.length() > 0)
- loadRBCoordinates(conf.inputRBCoordinates.val());
+ if (conf.restartRBCoordinates.length() > 0)
+ load_restart_coordinates(conf.restartRBCoordinates.val());
+ else if (conf.inputRBCoordinates.length() > 0)
+ loadRBCoordinates(conf.inputRBCoordinates.val());
random = new RandomCPU(conf.seed + repID + 1); /* +1 to avoid using same seed as RandomCUDA */
+
initializeForcePairs(); // Must run after construct_grids()
gpuErrchk(cudaDeviceSynchronize()); /* RBTODO: this should be extraneous */
-
- //Boltzmann distribution
- for (int i = 0; i < rigidBodyByType.size(); i++)
- {
- for (int j = 0; j < rigidBodyByType[i].size(); j++)
- {
- RigidBody& rb = rigidBodyByType[i][j];
- // thermostat
- rb.Boltzmann(seed);
- }
- }
}
RigidBodyController::~RigidBodyController() {
@@ -337,6 +329,9 @@ bool RigidBodyController::loadRBCoordinates(const char* fileName) {
rb.momentum = Vector3((float)strtod(tokenList[12],NULL), (float) strtod(tokenList[13],NULL), (float) strtod(tokenList[14],NULL));
rb.angularMomentum = Vector3((float)strtod(tokenList[15],NULL), (float) strtod(tokenList[16],NULL), (float) strtod(tokenList[17],NULL));
}
+
+ if(conf.RigidBodyDynamicType == String("Langevin") && numTokens < 18)
+ rb.Boltzmann(conf.seed);
delete[] tokenList;
@@ -352,6 +347,82 @@ bool RigidBodyController::loadRBCoordinates(const char* fileName) {
fclose(inp);
return true;
}
+bool RigidBodyController::load_restart_coordinates(const char* filename) {
+ char line[STRLEN];
+ FILE* inp = fopen(filename, "r");
+
+ if (inp == NULL) {
+ printf("ARBD: load RB coordinates: File '%s' does not exist\n", filename);
+ exit(-1);
+ }
+
+ int imax = rigidBodyByType.size();
+ int i = 0;
+ int jmax = rigidBodyByType[i].size();
+ int j = 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 < 2+3+9) {
+ printf("ARBD: invalid RB restart coordinate line: %s\n", line);
+ fclose(inp);
+ exit(-1);
+ }
+ if(conf.RigidBodyDynamicType == String("Langevin") && numTokens < 20)
+ {
+ std::cout << "Warning the initial momentum set by random number" << std::endl;
+ }
+
+ String* tokenList = new String[numTokens];
+ s.tokenize(tokenList);
+ if (tokenList == NULL) {
+ printf("ARBD: invalid RB restart coordinate line: %s\n", line);
+ fclose(inp);
+ exit(-1);
+ }
+
+ RigidBody& rb = rigidBodyByType[i][j];
+ printf("Assinging positions %d %d %f\n",i,j, (float) strtod(tokenList[2],NULL));
+ rb.position = Vector3(
+ (float) strtod(tokenList[2],NULL), (float) strtod(tokenList[3],NULL), (float) strtod(tokenList[4],NULL));
+ rb.orientation = Matrix3(
+ (float) strtod(tokenList[5],NULL), (float) strtod(tokenList[6],NULL), (float) strtod(tokenList[7],NULL),
+ (float) strtod(tokenList[8],NULL), (float) strtod(tokenList[9],NULL), (float) strtod(tokenList[10],NULL),
+ (float) strtod(tokenList[11],NULL), (float) strtod(tokenList[12],NULL), (float) strtod(tokenList[13],NULL));
+
+ if(conf.RigidBodyDynamicType == String("Langevin") && numTokens >= 20)
+ {
+ rb.momentum = Vector3((float)strtod(tokenList[14],NULL), (float) strtod(tokenList[15],NULL), (float) strtod(tokenList[16],NULL));
+ rb.angularMomentum = Vector3((float)strtod(tokenList[17],NULL), (float) strtod(tokenList[18],NULL), (float) strtod(tokenList[19],NULL));
+ }
+
+ if(conf.RigidBodyDynamicType == String("Langevin") && numTokens < 20)
+ rb.Boltzmann(conf.seed);
+
+ delete[] tokenList;
+
+ j++;
+ if (j == jmax) {
+ i++;
+ if (i == imax)
+ break;
+ j=0;
+ jmax = rigidBodyByType[i].size();
+ }
+ }
+ fclose(inp);
+ if (i < imax || j < jmax) {
+ printf("ARBD: RB restart file did not contain the correct number of lines: %s\n", filename);
+ exit(-1);
+ }
+ return true;
+}
diff --git a/src/RigidBodyController.h b/src/RigidBodyController.h
index ff99091..0e2dbad 100644
--- a/src/RigidBodyController.h
+++ b/src/RigidBodyController.h
@@ -117,6 +117,7 @@ public:
float getEnergy(float (RigidBody::*get)());
private:
bool loadRBCoordinates(const char* fileName);
+ bool load_restart_coordinates(const char* filename);
void initializeForcePairs();
//void print(int step);
--
GitLab