Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F78675231
workspace.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Aug 22, 08:24
Size
14 KB
Mime Type
text/x-c
Expires
Sat, Aug 24, 08:24 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
19612555
Attached To
rLAMMPS lammps
workspace.cpp
View Options
/*
*_________________________________________________________________________*
* POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE *
* DESCRIPTION: SEE READ-ME *
* FILE NAME: workspace.cpp *
* AUTHORS: See Author List *
* GRANTS: See Grants List *
* COPYRIGHT: (C) 2005 by Authors as listed in Author's List *
* LICENSE: Please see License Agreement *
* DOWNLOAD: Free at www.rpi.edu/~anderk5 *
* ADMINISTRATOR: Prof. Kurt Anderson *
* Computational Dynamics Lab *
* Rensselaer Polytechnic Institute *
* 110 8th St. Troy NY 12180 *
* CONTACT: anderk5@rpi.edu *
*_________________________________________________________________________*/
#include "workspace.h"
#include "system.h"
#include "solver.h"
#include "SystemProcessor.h"
#include <iostream>
#include <fstream>
#include <iomanip>
#include <cmath>
using namespace std;
void Workspace::allocateNewSystem() {
currentIndex++;
if(currentIndex < maxAlloc)
{
system[currentIndex].system = new System;
}
else
{
maxAlloc = (maxAlloc + 1) * 2;
SysData * tempPtrSys = new SysData[maxAlloc];
for(int i = 0; i < currentIndex; i++)
{
tempPtrSys[i] = system[i];
}
delete [] system;
system = tempPtrSys;
system[currentIndex].system = new System;
}
}
Workspace::Workspace(){
currentIndex = -1;
maxAlloc = 0;
system = NULL;
}
Workspace::~Workspace(){
for(int i = 0; i <= currentIndex; i++){
delete system[i].system;
}
delete [] system;
}
bool Workspace::LoadFile(char* filename){
bool ans;
ifstream file;
file.open(filename, ifstream::in);
if( !file.is_open() ){
cerr << "File '" << filename << "' not found." << endl;
return false;
}
allocateNewSystem();
ans = system[currentIndex].system->ReadIn(file);
file.close();
return ans;
}
void Workspace::SetLammpsValues(double dtv, double dthalf, double tempcon){
Thalf = dthalf;
Tfull = dtv;
ConFac = tempcon;
}
bool Workspace::MakeSystem(int& nbody, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space, int &njoint, int **&jointbody, double **&xjoint, int& nfree, int*freelist, double dthalf, double dtv, double tempcon, double KE){
SetLammpsValues(dtv, dthalf, tempcon);
if(njoint){
SystemProcessor sys;
sys.processArray(jointbody, njoint);
List<POEMSChain> * results = sys.getSystemData();
int numsyschains = results->GetNumElements();
int headvalue = 0;
List<POEMSChain> * newresults = results;
ListElement<POEMSChain> * tempNode = results->GetHeadElement();
int stop = 1;
int counter = 1;
for(int n = 1; n<=numsyschains; n++){
while(stop){
if ( (*(tempNode->value->listOfNodes.GetHeadElement()->value) == (headvalue+1) ) || (*(tempNode->value->listOfNodes.GetTailElement()->value) == (headvalue+1) ) ) {
newresults->Append(tempNode->value);
headvalue = headvalue + tempNode->value->listOfNodes.GetNumElements();
tempNode = results->GetHeadElement();
stop = 0;
counter ++;
}
else{
tempNode = tempNode->next;
}
}
stop=1;
}
ListElement<POEMSChain> * TNode = newresults->GetHeadElement();
ListElement<POEMSChain> * TTNode = newresults->GetHeadElement();
for(int kk=1; kk<=numsyschains; kk++){
if(kk!=numsyschains)
TTNode = TNode->next;
newresults->Remove(TNode);
if(kk!=numsyschains)
TNode = TTNode;
}
ListElement<POEMSChain> * NodeValue = newresults->GetHeadElement();
int count = 0;
int * array;
int ** arrayFromChain;
int numElementsInSystem;
int ttk = 0;
while(NodeValue != NULL) {
array = new int[NodeValue->value->listOfNodes.GetNumElements()];
arrayFromChain = NodeValue->value->listOfNodes.CreateArray();
numElementsInSystem = NodeValue->value->listOfNodes.GetNumElements();
for(counter = 0; counter < numElementsInSystem; counter++){
array[counter] = *arrayFromChain[counter];
}
SetKE(1,KE);
allocateNewSystem();
system[currentIndex].system->Create_System_LAMMPS(nbody,masstotal,inertia,xcm,xjoint,vcm,omega,ex_space,ey_space,ez_space, numElementsInSystem, array, count);
system[currentIndex].solver = ONSOLVER;
ttk = ttk + 1;
count = ttk;
delete [] array;
delete [] arrayFromChain;
NodeValue= NodeValue->next;
}
}
if(nfree){
MakeDegenerateSystem(nfree,freelist,masstotal,inertia,xcm,vcm,omega,ex_space,ey_space,ez_space);
}
return true;
}
bool Workspace::MakeDegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space){
allocateNewSystem();
system[currentIndex].system->Create_DegenerateSystem(nfree,freelist,masstotal,inertia,xcm,vcm,omega,ex_space,ey_space,ez_space);
system[currentIndex].solver = ONSOLVER;
return true;
}
bool Workspace::SaveFile(char* filename, int index){
if(index < 0){
index = currentIndex;
}
ofstream file;
file.open(filename, ofstream::out);
if( !file.is_open() ){
cerr << "File '" << filename << "' could not be opened." << endl;
return false;
}
if(index >= 0 && index <= currentIndex){
system[index].system->WriteOut(file);
}
else {
cerr << "Error, requested system index " << index << ", minimum index 0 and maximum index " << currentIndex << endl;
}
file.close();
return true;
}
System* Workspace::GetSystem(int index){
if(index <= currentIndex){
if(index >= 0){
return system[index].system;
}
else{
return system[currentIndex].system;
}
}
else{
return NULL;
}
}
void Workspace::AddSolver(Solver* s, int index){
if(currentIndex >= index){
if(index >= 0){
system[index].solver = (int)s->GetSolverType();
}
else{
system[currentIndex].solver = (int)s->GetSolverType();
}
}
else{
cout << "Error adding solver to index " << index << endl;
}
}
int Workspace::getNumberOfSystems(){
return currentIndex + 1;
}
void Workspace::SetKE(int temp, double SysKE){
KE_val = SysKE;
FirstTime =temp;
}
void Workspace::LobattoOne(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space){
int numsys = currentIndex;
int numbodies;
double time = 0.0;
int * mappings;
double SysKE=0.0;
for (int i = 0; i <= numsys; i++){
mappings = system[i].system->GetMappings();
numbodies = system[i].system->GetNumBodies() - 1;
Matrix FF(6,numbodies);
FF.Zeros();
for (int j=1; j<=numbodies; j++){
FF(1,j) = torque[mappings[j - 1]-1][0]*ConFac;
FF(2,j) = torque[mappings[j - 1]-1][1]*ConFac;
FF(3,j) = torque[mappings[j - 1]-1][2]*ConFac;
FF(4,j) = fcm[mappings[j - 1]-1][0]*ConFac;
FF(5,j) = fcm[mappings[j - 1]-1][1]*ConFac;
FF(6,j) = fcm[mappings[j - 1]-1][2]*ConFac;
}
//------------------------------------//
// Get a solver and solve that system.
Solver * theSolver = Solver::GetSolver((SolverType)system[i].solver);
theSolver->SetSystem(system[i].system);
theSolver->Solve(time, FF);
theSolver->Solve(time, FF);
ColMatrix tempx = *((*theSolver).GetState());
ColMatrix tempv = *((*theSolver).GetStateDerivative());
ColMatrix tempa = *((*theSolver).GetStateDerivativeDerivative());
for(int numint =0 ; numint<3; numint++){
theSolver->Solve(time, FF);
tempa = *((*theSolver).GetStateDerivativeDerivative());
*((*theSolver).GetStateDerivative())= tempv + Thalf*tempa;
}
ColMatrix TempV= *((*theSolver).GetStateDerivative());
*((*theSolver).GetState())= tempx + Tfull*TempV;
int numjoints = system[i].system->joints.GetNumElements();
for(int k = 0; k < numjoints; k++){
system[i].system->joints(k)->ForwardKinematics();
}
for(int k = 0; k < numbodies; k++){
Vect3 temp1 =system[i].system->bodies(k+1)->r;
Vect3 temp2 =system[i].system->bodies(k+1)->v;
Vect3 temp3 =system[i].system->bodies(k+1)->omega;
Mat3x3 temp4 =system[i].system->bodies(k+1)->n_C_k;
for(int m = 0; m < 3; m++){
xcm[mappings[k]-1][m] = temp1(m+1);
vcm[mappings[k]-1][m] = temp2(m+1);
omega[mappings[k]-1][m] = temp3(m+1);
ex_space[mappings[k]-1][m] = temp4(m+1,1);
ey_space[mappings[k]-1][m] = temp4(m+1,2);
ez_space[mappings[k]-1][m] = temp4(m+1,3);
}
SysKE = SysKE + system[i].system->bodies(k+1)->KE;
}
delete theSolver;
}
}
void Workspace::LobattoTwo(double **&vcm,double **&omega,double **&torque, double **&fcm){
int numsys = currentIndex;
int numbodies;
double time = 0.0;
int * mappings;
double SysKE =0.0;
for (int i = 0; i <= numsys; i++){
mappings = system[i].system->GetMappings();
numbodies = system[i].system->GetNumBodies() - 1;
Matrix FF(6,numbodies);
for (int j=1; j<=numbodies; j++){
FF(1,j) = torque[mappings[j - 1]-1][0]*ConFac;
FF(2,j) = torque[mappings[j - 1]-1][1]*ConFac;
FF(3,j) = torque[mappings[j - 1]-1][2]*ConFac;
FF(4,j) = fcm[mappings[j - 1]-1][0]*ConFac;
FF(5,j) = fcm[mappings[j - 1]-1][1]*ConFac;
FF(6,j) = fcm[mappings[j - 1]-1][2]*ConFac;
}
//------------------------------------//
// Get a solver and solve that system.
Solver * theSolver = Solver::GetSolver((SolverType)system[i].solver);
theSolver->SetSystem(system[i].system);
theSolver->Solve(time, FF);
ColMatrix tempv = *((*theSolver).GetStateDerivative());
ColMatrix tempa = *((*theSolver).GetStateDerivativeDerivative());
*((*theSolver).GetStateDerivative()) = tempv + Thalf*tempa;
int numjoints = system[i].system->joints.GetNumElements();
for(int k = 0; k < numjoints; k++){
system[i].system->joints(k)->ForwardKinematics();
}
for(int k = 0; k < numbodies; k++){
Vect3 temp1 =system[i].system->bodies(k+1)->r;
Vect3 temp2 =system[i].system->bodies(k+1)->v;
Vect3 temp3 =system[i].system->bodies(k+1)->omega;
SysKE = SysKE + system[i].system->bodies(k+1)->KE;
for(int m = 0; m < 3; m++){
vcm[mappings[k]-1][m] = temp2(m+1);
omega[mappings[k]-1][m] = temp3(m+1);
}
}
delete theSolver;
}
}
void Workspace::RKStep(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space){
double a[6];
double b[6][6];
double c[6];
//double e[6];
a[1] = 0.2;
a[2] = 0.3;
a[3] = 0.6;
a[4] = 1.0;
a[5] = 0.875;
b[1][0] = 0.2;
b[2][0] = 0.075; b[2][1] = 0.225;
b[3][0] = 0.3; b[3][1] = -0.9; b[3][2] = 1.2;
b[4][0] = -11.0/54.0; b[4][1] = 2.5; b[4][2] = -70.0/27.0; b[4][3] = 35.0/27.0;
b[5][0] = 1631.0/55296.0; b[5][1] = 175.0/512.0; b[5][2] = 575.0/13824.0; b[5][3] = 44275.0/110592.0; b[5][4] = 253.0/4096.0;
c[0] = 37.0/378.0;
c[1] = 0.0;
c[2] = 250.0/621.0;
c[3] = 125.0/594.0;
c[4] = 0.0;
c[5] = 512.0/1771.0;
int numsys = currentIndex;
int numbodies;
double time = 0.0;
int * mappings;
double SysKE =0.0;
for (int i = 0; i <= numsys; i++){
mappings = system[i].system->GetMappings();
numbodies = system[i].system->GetNumBodies() - 1;
Matrix FF(6,numbodies);
for (int j=1; j<=numbodies; j++){
FF(1,j) = ConFac*torque[mappings[j - 1]-1][0];
FF(2,j) = ConFac*torque[mappings[j - 1]-1][1];
FF(3,j) = ConFac*torque[mappings[j - 1]-1][2];
FF(4,j) = ConFac*fcm[mappings[j - 1]-1][0];
FF(5,j) = ConFac*fcm[mappings[j - 1]-1][1];
FF(6,j) = ConFac*fcm[mappings[j - 1]-1][2];
}
//------------------------------------//
// Get a solver and solve that system.
Solver * theSolver = Solver::GetSolver((SolverType)system[i].solver);
theSolver->SetSystem(system[i].system);
theSolver->Solve(time, FF);
ColMatrix initial_x;
ColMatrix initial_xdot;
ColMatMap* x;
ColMatMap* xdot;
ColMatMap* xdotdot;
x = theSolver->GetState();
xdot = theSolver->GetStateDerivative();
xdotdot=theSolver->GetStateDerivativeDerivative();
initial_x = *x;
initial_xdot = *xdot;
ColMatrix f[6];
ColMatrix ff[6];
ff[0] = initial_xdot;
f[0] = *xdotdot;
for(int ii=1;ii<6;ii++){
time = a[ii] * Tfull;
(*x) = initial_x;
(*xdot) = initial_xdot;
for(int j=0;j<ii;j++){
(*x) = (*x) + (b[ii][j]*Tfull)*ff[j];
(*xdot) = (*xdot) + (b[ii][j]*Tfull)*f[j];
}
theSolver->Solve(time,FF);
f[ii] = (*xdotdot);
ff[ii] = (*xdot);
}
(*x) = initial_x + (c[0]*Tfull)*ff[0] + (c[2]*Tfull)*ff[2] + (c[3]*Tfull)*ff[3] + (c[5]*Tfull)*ff[5];
(*xdot) = initial_xdot + (c[0]*Tfull)*f[0] + (c[2]*Tfull)*f[2] + (c[3]*Tfull)*f[3] + (c[5]*Tfull)*f[5];
int numjoints = system[i].system->joints.GetNumElements();
for(int k = 0; k < numjoints; k++){
system[i].system->joints(k)->ForwardKinematics();
}
for(int k = 0; k < numbodies; k++){
Vect3 temp1 =system[i].system->bodies(k+1)->r;
Vect3 temp2 =system[i].system->bodies(k+1)->v;
Vect3 temp3 =system[i].system->bodies(k+1)->omega;
Mat3x3 temp4 =system[i].system->bodies(k+1)->n_C_k;
SysKE = SysKE + system[i].system->bodies(k+1)->KE;
for(int m = 0; m < 3; m++){
xcm[mappings[k]-1][m] = temp1(m+1);
vcm[mappings[k]-1][m] = temp2(m+1);
omega[mappings[k]-1][m] = temp3(m+1);
ex_space[mappings[k]-1][m] = temp4(m+1,1);
ey_space[mappings[k]-1][m] = temp4(m+1,2);
ez_space[mappings[k]-1][m] = temp4(m+1,3);
}
}
delete theSolver;
}
}
void Workspace::WriteFile(char * filename){
int numsys = currentIndex;
int numbodies;
for (int i = 0; i <= numsys; i++){
numbodies = system[i].system->GetNumBodies() - 1;
ofstream outfile;
outfile.open(filename,ofstream::out | ios::app);
outfile << numbodies<<endl;
outfile << "Atoms "<<endl;
for(int k = 0; k < numbodies; k++){
Vect3 temp1 =system[i].system->bodies(k+1)->r;
outfile<<1<<"\t"<<temp1(1)<<"\t"<<temp1(2)<<"\t"<<temp1(3)<<endl;
}
outfile.close();
}
}
Event Timeline
Log In to Comment