lammps/lib/poems/workspace.cpp

/*
 *_________________________________________________________________________*
 *      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();
	}	
  }