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dataExtraction.h
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dataExtraction.h
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/**
* \brief Data extraction while the program runs.
* This is the data extraction header. It is currently used for molecular dynamics
* (see MD.cpp), but it is probably general enough for other usage, like DPD. This
* is a user modifiable header that can extract quantities like kinetic or potential
* energy, center of mass, tension, etc... Some objects are defined twice, once here
* and once in MD.cpp; that shouldn't be a problem unless you run out of memory. The
* basic usage of this is as follows:
* 1. Build your system and this object.
* 2. Initialize some values.
* 3. Run MD until measure interval is complete.
* 4. Execute the compute member function of this object.
* 5. repeat step 2 unless system is done.
* 6. Destroy objects and exit.
*
* What you are modifying here is three parts:
* 1. The constructor member is run during build phase (step 1 above).
* 2. The initialize member is run during initialization (step 2 above).
* 2. The compute member is executed every measure interval (step 4 above).\n
* 3. The destructor member is run prior to exiting (step 6 above).
*
* Also, note that you are passing the blob object into the object's constructor; so
* at an interval, you should have all the information about the system.
*
* This is also a template. T is the numeric type (float, double, int, etc...) and
* U is the system blob type (see systemMD.h and systemDPD.h for an example of the blob).
*
* If you plan on modifying the object, then you should probably put quickly computed
* variables in the compute member, and persistent variables, which require information
* from the previous steps, as private members of this object.
*/
template <typename T, typename U>
class dataExtraction {
public:
/**
* The constructor, where blob is a pointer (don't forget the reference operator (&)!)
* and name is a pointer to a '\0' terminated char string. Execute this after you build
* the system (after reading in an mpd file, for example).
*/
dataExtraction(U *blob, char *name);
/**
* Alternative constructor, where blob is a pointer (don't forget the reference operator (&)!)
* and name is a pointer to a '\0' terminated char string. Execute this after you build
* the system (after reading in an mpd file, for example). Also accepts the absolute position
* of a particle list, so that you can track diffusion.
*/
dataExtraction(U *blob, char *name, position<T> *absolutePosition);
/**
* The destructor, where old memory goes to die. This should be executed after it falls
* out of scope, like when a function (e.g. main()) exits.
*/
~dataExtraction();
/**
* An initialize member. Call this after you build it. It automatically calls compute too.
* Mainly, it just does some extra setup prior to your molecular dynamics loop.
*/
void initialize();
/**
* This does some computations faster. Data extraction is still put off until compute is called.
*/
void computeFast();
/**
* A compute member. Call this every measure interval to update the data extraction. When
* you modify it, don't forget to close files when you are done using them. Typical extraction
* is as follows:
* 1. Set values you want.
* 2. Compute against data in the system blob.
* 3. Open a file.
* 4. Write computed data to the file.
* 5. Close the file.
*
* Although, you could swap steps 2 and 3.
*/
void compute();
/**
* Starts calculation of diffusion.
*/
void startDiffusion();
#ifdef ANCHOR_DATA
/**
* An extra member to view the current state of a parameter. I use this to cut the simulation
* short if there are too many anchors broken. I recommend adding whatever you want.
* Not active unless ANCHOR type is defined!
*/
int readNAnchors()
{
return nAnchor;
};
/**
* An extra member to view the current state of a parameter. I use this to cut the simulation
* short if there are too many anchors broken. I recommend adding whatever you want.
* Not active unless ANCHOR type is defined!
*/
int readNBrokenAnchors()
{
return nBroken;
};
#endif
private:
//These variables are typically set during construction:
//The system blob.
U *System;
//The name of the system.
char *name;
//Non-bonded pair interactions. Persistant object, but you have to execute
//the build member prior to use.
//See 'include/algorithms/cellOpt.h'.
CellOpt<T, Potential<T>, Force <T> > pairInteractions;
//An object that computes kinetic energy. Doesn't really need to be persistent.
//See 'include/algorithms/dataCollection.h'.
Kinetic<T> kinetic;
//Tracks the kinetic energy density distribution as a histagram
std::vector<int> kEnergyDensity;
T kEnergyDensityPartition;//actual length of energy ranges
//An object that computes inner volumes. This one is quite complex.
//See 'include/algorithms/volume.h'.
//VolumeExtraction<T> volumize;
//An object for locating neighbors with cell lists. (Standard neighbor list for system)
//See 'include/algorithms/cell.h'.
Cell<T> neighbors;
//An object for getting nearby bleb particles. (Different indices)
//See 'include/algorithms/cell.h'.
Cell<T> blebNeighbors;
//A stack for recursion.
int *stack;
//Flags for our stack.
int *flag;
//Bleb particle indices.
int *blebParticles;
//Flip flop object? (nComponents, inner ratio, outer ratio, ...)
//Useful references for past (persistent) data
//#ifdef SOLVENT
//Number of particles exchanged between inside and outside.
//Need to know what it was before to compare.
int nExchanged;
//#endif
//For flip flop rate calculations?
//bool *flipFlop;
#ifdef ANCHOR_DATA
//A list of anchor indices. Not necessarily persistent, just difficult to compute
//in large systems.
int *anchorIndex;
//Tracks broken anchors.
bool *brokenAnchor;
//Total number of anchors.
int nAnchor;
//Total number of broken anchors
int nBroken;
//Indices of clusters.
int *clusterIndices;
//Initial anchor distance.
T initialAnchorDistance;
//Average anchor distance.
T anchorDistance;
//A vector containing all anchor connections, shares indices with anchorIndex above.
std::vector< std::vector <int> > anchorConnections;
//A vector containing all anchor and cytoskeleton particles, We are using this in
// place of a neighbor list under the assumption that there are far fewer cytoskeleton
// particles than there are neighbors when we search for exclusions.
std::vector<int> cytoAnchorList;
//Track mean squared displacement of cytoskeleton anchor, for execluded volume.
std::vector< std::vector<T> > msCytoAnchor;
//Track number of mean square displacement datapoints.
int nMSCytoAnchorSteps;
//Old anchor positions
std::vector< position<T> > oldAnchorPositions;
//list of cytoskeleton molecules
std::vector<int> cytoList;
#endif
#ifdef FLAT_MEMBRANE
//Height map for flat membrane fluctuations.
T *heightMap;
//Height map number of elements per cell.
T *heightMapElements;
//Number of heightMap cells projected onto the Z plane.
twoVector<int> heightMapCells;
//Size of each heightMap Cell.
twoVector<T> heightMapCellSize;
#endif
#ifdef NANOPARTICLE
int nanoParticleOffset;
int nNanoParticleElements;
#endif
//For diffusion, it is the absolute position of a particle (no pbc)
position<T> *aP;
//For diffusion, stores the start positions and signifies the start of diffusion calculations
position<T> *aPStart;
};
template <typename T, typename U>
dataExtraction<T,U>::dataExtraction(U *blob, char *name, position<T> *absolutePosition)
{
System=blob;
this->name=name;
//initialize data structures here, some of these are created twice per execution (once in main, once here)
kinetic.initialize((*System).getVelocities(), (*System).readNParticles());
//potential info
pairInteractions.initialize((*System).getPositions(), (*System).getAccelerations(),
(*System).getTwoBodyFconst(), (*System).getTwoBodyUconst(), (*System).readNParticles(),
(*System).readNTypes(), (*System).readSize(), (*System).readPeriodic(), (*System).readCutoff());
//For volume
//int *excludeType=new int[(*System).readNTypes()];
//for(int i=1;i<(*System).readNTypes();i++)
// excludeType[i-1]=i;
//volumize.initialize((*System).getPositions(), (*System).readNParticles(), (*System).readSize(),
// (*System).readCutoff(), excludeType, (*System).readNTypes()-1, (*System).readSeed());
//delete excludeType;
//neighbor list
neighbors.initialize((*System).getPositions(), (*System).readNParticles(), (*System).readCutoff(), (*System).readSize());
#ifdef ANCHOR_DATA
nAnchor=0;
//count number of anchors
for(int i=0;i<(*System).readNParticles();i++)
{
if((*System).getPositions()[i].type==ANCHOR)
nAnchor++;
if((*System).getPositions()[i].type==ANCHOR || (*System).getPositions()[i].type==CYTO)
cytoAnchorList.push_back(i);
}
if(nAnchor!=0)
{
anchorIndex=new int[nAnchor];
brokenAnchor=new bool[nAnchor];
}
else
{
brokenAnchor=NULL;
anchorIndex=NULL;
}
nAnchor=0;
//Fill anchor indices
for(int i=0;i<(*System).readNParticles();i++)
if((*System).getPositions()[i].type==ANCHOR)
anchorIndex[nAnchor++]=i;
//For cluster finding during blebbing
stack=new int[(*System).readNParticles()];
flag=new int[(*System).readNParticles()];
blebParticles=new int[(*System).readNParticles()];
blebNeighbors.initialize((*System).getPositions(), (*System).readNParticles(), (*System).readCutoff(), \
(*System).readSize(), blebParticles, (*System).readNParticles());
for(int i=0;i<(*System).readNMolecules();i++)
{
bool containsCyto=false;
//pick a structure by type
switch((*System).getMolecule()[i].readType())
{
case BOND:
{
for(int l=0;l<(*System).getMolecule()[i].readNBond();l++)
{
//These are the first and second particles of the bond
int firstParticle=(*System).getMolecule()[i].getBonds()[l].s[0];
int secondParticle=(*System).getMolecule()[i].getBonds()[l].s[1];
if((*System).getPositions()[firstParticle].type==CYTO ||
(*System).getPositions()[firstParticle].type==ANCHOR ||
(*System).getPositions()[firstParticle].type==MONOMER)
containsCyto=true;
if((*System).getPositions()[secondParticle].type==CYTO ||
(*System).getPositions()[secondParticle].type==ANCHOR ||
(*System).getPositions()[secondParticle].type==MONOMER)
containsCyto=true;
}
break;
}
case BEND:
{
for(int l=0;l<(*System).getMolecule()[i].readNBond();l++)
{
//These are the first and second particles of the bond
int firstParticle=(*System).getMolecule()[i].getBonds()[l].s[0];
int secondParticle=(*System).getMolecule()[i].getBonds()[l].s[1];
int thirdParticle=(*System).getMolecule()[i].getBonds()[l].s[2];
if((*System).getPositions()[firstParticle].type==CYTO ||
(*System).getPositions()[firstParticle].type==ANCHOR ||
(*System).getPositions()[firstParticle].type==MONOMER)
containsCyto=true;
if((*System).getPositions()[secondParticle].type==CYTO ||
(*System).getPositions()[secondParticle].type==ANCHOR ||
(*System).getPositions()[secondParticle].type==MONOMER)
containsCyto=true;
if((*System).getPositions()[thirdParticle].type==CYTO ||
(*System).getPositions()[thirdParticle].type==ANCHOR ||
(*System).getPositions()[thirdParticle].type==MONOMER)
containsCyto=true;
}
break;
}
case CHAIN:
{
//Go through all bond descriptions
for(int l=0;l<(*System).getMolecule()[i].readNBond();l++)
{
fourVector<int> *bond=(*System).getMolecule()[i].getBonds();
//bond info
int start=bond[l].s[START];
int nChains=bond[l].s[NCHAINS];
int length=bond[l].s[CHAINLENGTH];
//go through all chain lengths
for(int k=start; k<start+length*nChains; k++)
{
if((*System).getPositions()[k].type==CYTO ||
(*System).getPositions()[k].type==ANCHOR ||
(*System).getPositions()[k].type==MONOMER)
containsCyto=true;
}
}
break;
}
default:
{
//does nothing
break;
}
}
if(containsCyto)
cytoList.push_back(i);
}
#endif
#ifdef FLAT_MEMBRANE
heightMapCells.x=256;
heightMapCells.y=256;
heightMapCellSize.x=(*System).readSize().x/T(heightMapCells.x);
heightMapCellSize.y=(*System).readSize().y/T(heightMapCells.y);
heightMap=new T[heightMapCells.x*heightMapCells.y];
heightMapElements=new T[heightMapCells.x*heightMapCells.y];
#endif
aP=absolutePosition;
aPStart=NULL;
kEnergyDensityPartition=0.0001;
}
template <typename T, typename U>
dataExtraction<T,U>::dataExtraction(U *blob, char *name)
{
System=blob;
this->name=name;
//initialize data structures here, some of these are created twice per execution (once in main, once here)
kinetic.initialize((*System).getVelocities(), (*System).readNParticles());
//potential info
pairInteractions.initialize((*System).getPositions(), (*System).getAccelerations(),
(*System).getTwoBodyFconst(), (*System).getTwoBodyUconst(), (*System).readNParticles(),
(*System).readNTypes(), (*System).readSize(), (*System).readPeriodic(), (*System).readCutoff());
//For volume
//int *excludeType=new int[(*System).readNTypes()];
//for(int i=1;i<(*System).readNTypes();i++)
// excludeType[i-1]=i;
//volumize.initialize((*System).getPositions(), (*System).readNParticles(), (*System).readSize(),
// (*System).readCutoff(), excludeType, (*System).readNTypes()-1, (*System).readSeed());
//delete excludeType;
//neighbor list
neighbors.initialize((*System).getPositions(), (*System).readNParticles(), (*System).readCutoff(), (*System).readSize());
#ifdef ANCHOR_DATA
nAnchor=0;
//count number of anchors
for(int i=0;i<(*System).readNParticles();i++)
{
if((*System).getPositions()[i].type==ANCHOR)
nAnchor++;
if((*System).getPositions()[i].type==ANCHOR || (*System).getPositions()[i].type==CYTO)
cytoAnchorList.push_back(i);
}
if(nAnchor!=0)
{
anchorIndex=new int[nAnchor];
brokenAnchor=new bool[nAnchor];
}
else
{
brokenAnchor=NULL;
anchorIndex=NULL;
}
nAnchor=0;
//Fill anchor indices
for(int i=0;i<(*System).readNParticles();i++)
if((*System).getPositions()[i].type==ANCHOR)
anchorIndex[nAnchor++]=i;
//For cluster finding during blebbing
stack=new int[(*System).readNParticles()];
flag=new int[(*System).readNParticles()];
blebParticles=new int[(*System).readNParticles()];
blebNeighbors.initialize((*System).getPositions(), (*System).readNParticles(), (*System).readCutoff(), \
(*System).readSize(), blebParticles, (*System).readNParticles());
for(int i=0;i<(*System).readNMolecules();i++)
{
bool containsCyto=false;
//pick a structure by type
switch((*System).getMolecule()[i].readType())
{
case BOND:
{
for(int l=0;l<(*System).getMolecule()[i].readNBond();l++)
{
//These are the first and second particles of the bond
int firstParticle=(*System).getMolecule()[i].getBonds()[l].s[0];
int secondParticle=(*System).getMolecule()[i].getBonds()[l].s[1];
if((*System).getPositions()[firstParticle].type==CYTO ||
(*System).getPositions()[firstParticle].type==ANCHOR ||
(*System).getPositions()[firstParticle].type==MONOMER)
containsCyto=true;
if((*System).getPositions()[secondParticle].type==CYTO ||
(*System).getPositions()[secondParticle].type==ANCHOR ||
(*System).getPositions()[secondParticle].type==MONOMER)
containsCyto=true;
}
break;
}
case BEND:
{
for(int l=0;l<(*System).getMolecule()[i].readNBond();l++)
{
//These are the first and second particles of the bond
int firstParticle=(*System).getMolecule()[i].getBonds()[l].s[0];
int secondParticle=(*System).getMolecule()[i].getBonds()[l].s[1];
int thirdParticle=(*System).getMolecule()[i].getBonds()[l].s[2];
if((*System).getPositions()[firstParticle].type==CYTO ||
(*System).getPositions()[firstParticle].type==ANCHOR ||
(*System).getPositions()[firstParticle].type==MONOMER)
containsCyto=true;
if((*System).getPositions()[secondParticle].type==CYTO ||
(*System).getPositions()[secondParticle].type==ANCHOR ||
(*System).getPositions()[secondParticle].type==MONOMER)
containsCyto=true;
if((*System).getPositions()[thirdParticle].type==CYTO ||
(*System).getPositions()[thirdParticle].type==ANCHOR ||
(*System).getPositions()[thirdParticle].type==MONOMER)
containsCyto=true;
}
break;
}
case CHAIN:
{
//Go through all bond descriptions
for(int l=0;l<(*System).getMolecule()[i].readNBond();l++)
{
fourVector<int> *bond=(*System).getMolecule()[i].getBonds();
//bond info
int start=bond[l].s[START];
int nChains=bond[l].s[NCHAINS];
int length=bond[l].s[CHAINLENGTH];
//go through all chain lengths
for(int k=start; k<start+length*nChains; k++)
{
if((*System).getPositions()[k].type==CYTO ||
(*System).getPositions()[k].type==ANCHOR ||
(*System).getPositions()[k].type==MONOMER)
containsCyto=true;
}
}
break;
}
default:
{
//does nothing
break;
}
}
if(containsCyto)
cytoList.push_back(i);
}
#endif
#ifdef FLAT_MEMBRANE
heightMapCells.x=256;
heightMapCells.y=256;
heightMapCellSize.x=(*System).readSize().x/float(heightMapCells.x);
heightMapCellSize.y=(*System).readSize().y/float(heightMapCells.y);
heightMap=new T[heightMapCells.x*heightMapCells.y];
heightMapElements=new T[heightMapCells.x*heightMapCells.y];
#endif
aP=NULL;
aPStart=NULL;
kEnergyDensityPartition=0.0001;
}
template <typename T, typename U>
dataExtraction<T,U>::~dataExtraction()
{
std::fstream dataFile;
std::string buf("kEnergyDensity_");
buf+=name;
buf+=".dat";
dataFile.open(buf.c_str(), std::ios::out);
long int partitionSum=0;
for(int i=0;i<kEnergyDensity.size();i++)
partitionSum+=kEnergyDensity[i];
for(int i=0;i<kEnergyDensity.size();i++)
{
dataFile << static_cast<float>(i)*kEnergyDensityPartition << '\t';
dataFile << static_cast<float>(kEnergyDensity[i])/static_cast<float>(partitionSum) << std::endl;
}
dataFile.close();
#ifdef ANCHOR_DATA
if(anchorIndex!=NULL)
delete anchorIndex;
if(brokenAnchor!=NULL)
delete brokenAnchor;
if(stack!=NULL)
delete stack;
if(flag!=NULL)
delete flag;
if(blebParticles!=NULL)
delete blebParticles;
#endif
#ifdef FLAT_MEMBRANE
if(heightMap!=NULL)
delete heightMap;
if(heightMapElements!=NULL)
delete heightMapElements;
#endif
if(aPStart!=NULL)
delete aPStart;
}
template <typename T, typename U>
void dataExtraction<T,U>::initialize()
{
//do initial data collection here (usually before system is run)
nExchanged=0;
//useful references
position<T> *p=(*System).getPositions();
threeVector<T> *v=(*System).getVelocities();
threeVector<T> *a=(*System).getAccelerations();
threeVector<T> s=(*System).readSize();
T cutoffSqr=(*System).readCutoff();
cutoffSqr*=cutoffSqr;
#ifdef ANCHOR_DATA
if(nAnchor>0)
{
int nConnections=0;
//let's just assume no anchors are broken when it starts
for(int i=0;i<nAnchor;i++)
brokenAnchor[i]=false;
//quick molecule access
molecule<T, fourVector<int> > *m=(*System).getMolecule();
initialAnchorDistance=0;
//Quick overview of what will be done:
// 1. Find a list of BOND types that contains the anchor.
// 2. Find a all CHAINs that contain the anchor's bonded particle (likely a cytoskeleton chain).
// 3. Find a BOND type that contains the CHAIN type's other end.
// 4. Check if it is bonded to another anchor.
// 5. Determine the distance between that anchor and the current anchor.
//Note: this assumes each chain that connects anchors is unique!
//check initial distance between anchors.
//This is deeply nested, but should be fairly quick because there are far fewer anchors and
// chains than particles in the system.
for(int anchor=0;anchor<nAnchor;anchor++)
{
std::vector<int> connected;
//1. Find a BOND type that contains the anchor.
for(int mol=0;mol<(*System).readNMolecules();mol++)
{
if(m[mol].readType()==BOND)
{
//reset every time we start a new search
m[mol].resetFind();
for(twoVector<int> buf=m[mol].findBond(anchorIndex[anchor]);buf.x!=-1;buf=m[mol].findBond(anchorIndex[anchor]))
{
//We found a bond
if(buf.x!=-1)
{
//we will push back the current cytoskeleton chain start particle
if(buf.y==0)
connected.push_back(m[mol].getBonds()[buf.x].s[1]);
else
connected.push_back(m[mol].getBonds()[buf.x].s[0]);
}
}
}
}
//2. Find a CHAIN type that contains the anchor's bonded particle
for(int mol=0;mol<(*System).readNMolecules();mol++)
{
if(m[mol].readType()==CHAIN)
{
//do it for each connected chain particle
for(int i=0;i<connected.size();i++)
{
//reset every time we start a new search
m[mol].resetFind();
twoVector<int> buf=m[mol].findBond(connected[i]);
//We found a chain
if(buf.x!=-1)
{
int start=m[mol].getBonds()[buf.x].s[START];
int length=m[mol].getBonds()[buf.x].s[CHAINLENGTH];
//we will adjust this to the the other end of the chain.
if((connected[i]-start)%length==0)
connected[i]+=(length);//connected[i] is at the beginning, grab the one at the end.
else
connected[i]-=(length);//connected[i] is at the end, grab the one at the beginning.
}
else
{
#ifdef WARNINGS_ENABLED
//std::cout << "Warning (dataExtraction): Can't locate chain!\n";
#endif
}
}
}
}
//3. Find a BOND type that contains the CHAIN type's other end.
for(int mol=0;mol<(*System).readNMolecules();mol++)
{
if(m[mol].readType()==BOND)
{
//do it for each connected chain particle
for(int i=0;i<connected.size();i++)
{
//reset every time we start a new search
m[mol].resetFind();
twoVector<int> buf=m[mol].findBond(connected[i]);
//We found a bond
if(buf.x!=-1)
{
//we will push back the current cytoskeleton chain start particle
if(buf.y==0)
connected[i]=m[mol].getBonds()[buf.x].s[1];
else
connected[i]=m[mol].getBonds()[buf.x].s[0];
}
else
{
#ifdef WARNINGS_ENABLED
//std::cout << "Warning (dataExtraction): Can't locate other anchor!\n";
#endif
}
}
}
}
//4. Check if it is bonded to another anchor.
for(int i=0;i<connected.size();i++)
if(p[connected[i]].type!=ANCHOR)//is it an anchor?
connected.erase(connected.begin()+i);//it isn't an anchor, remove it
//We don't have to repeat the above for every compute() call, only the 5th step is repeated in compute().
anchorConnections.push_back(connected);
//5. Determine the distance between that anchor and the current anchor.
for(int i=0;i<anchorConnections[anchor].size();i++)
{
threeVector<T> d;
//calculate bond length using minimum image
d.x=p[anchorIndex[anchor]].x-p[anchorConnections[anchor][i]].x;
d.y=p[anchorIndex[anchor]].y-p[anchorConnections[anchor][i]].y;
d.z=p[anchorIndex[anchor]].z-p[anchorConnections[anchor][i]].z;
if(d.x>=s.x/2.0) d.x-=s.x;
if(d.x<=-s.x/2.0) d.x+=s.x;
if(d.y>=s.y/2.0) d.y-=s.y;
if(d.y<=-s.y/2.0) d.y+=s.y;
if(d.z>=s.z/2.0) d.z-=s.z;
if(d.z<=-s.z/2.0) d.z+=s.z;
anchorDistance+=sqrt(d.x*d.x+d.y*d.y+d.z*d.z);
nConnections++;
}
}
if(nConnections>0)
anchorDistance/=float(nConnections);
else
anchorDistance=1.0;
initialAnchorDistance=anchorDistance;
if(initialAnchorDistance<10.0)//There is a thickness associated with the bilayer, this 2x that thickness
initialAnchorDistance=10.0;
std::cout << "Using anchor to anchor distance for bleb search cutoff: " << initialAnchorDistance << '\n';
std::cout << "There are " << nAnchor << " anchors.\n";
//Initialize mean square displacement
if(aP!=NULL)
{
for(int i=0;i<nAnchor;i++)
msCytoAnchor.push_back(std::vector<T>());
for(int i=0;i<nAnchor;i++)
oldAnchorPositions.push_back(aP[cytoAnchorList[i]]);
nMSCytoAnchorSteps=0;
}
}
#endif
#ifdef NANOPARTICLE
nanoParticleOffset=-1;
nNanoParticleElements=0;
for(int i=0;i<(*System).readNParticles();i++)
{
if(p[i].type==NANOPARTICLE && nanoParticleOffset==-1)
{
nanoParticleOffset=i;
}
if(p[i].type!=NANOPARTICLE && nanoParticleOffset>=0)
{
nNanoParticleElements=i-nanoParticleOffset;
break;
}
}
if(nNanoParticleElements==0)
nNanoParticleElements=(*System).readNParticles()-nanoParticleOffset;
#endif
}
template <typename T, typename U>
void dataExtraction<T,U>::startDiffusion()
{
if(aP!=NULL && aPStart==NULL)
{
aPStart=new position<T>[(*System).readNParticles()];
for(int i=0;i<(*System).readNParticles();i++)
{
aPStart[i]=aP[i];
//Alternative version (Doesn't work the same way!):
//aPStart[i]=(*System).getPositions()[i];
}
}
}
template <typename T, typename U>
void dataExtraction<T,U>::computeFast()
{
#ifdef ANCHOR_DATA
/*
//track anchor deviation
if(aP!=NULL)
{
for(int i=0;i<nAnchor;i++)
{
//Compute the MSD from their start
threeVector<T> d;
d.x=aP[cytoAnchorList[i]].x-oldAnchorPositions[i].x;
d.y=aP[cytoAnchorList[i]].y-oldAnchorPositions[i].y;
d.z=aP[cytoAnchorList[i]].z-oldAnchorPositions[i].z;
msCytoAnchor[i].push_back(sqrt(d.x*d.x+d.y*d.y+d.z*d.z));
}
}
*/
#endif
}
template <typename T, typename U>
void dataExtraction<T,U>::compute()
{
//useful references
position<T> *p=(*System).getPositions();
threeVector<T> *v=(*System).getVelocities();
threeVector<T> *a=(*System).getAccelerations();
threeVector<T> s=(*System).readSize();
T cutoffSqr=(*System).readCutoff();
cutoffSqr*=cutoffSqr;
//Cuda works for this
pairInteractions.resize((*System).readSize());//Can't forget this!
pairInteractions.build();
T potential=pairInteractions.computePotential();
//Cuda does not work on this loop yet
//Better version of molecule interactions
T lBond=0;
int nBond=0;
T costhetaBend=0;
int nBend=0;
twoVector<T> lBend;
lBend.x=0;
lBend.y=0;
T beadPotential=0;
int nBeads=0;
//Go through all molecule structures
for(int k=0;k<(*System).readNMolecules();k++)
{
//pick a structure by type
switch((*System).getMolecule()[k].readType())
{
case BOND:
{
potential+=(*System).doBondPotential(k);
//Go through all in bond list
T lBondPrivate=0;
//#pragma omp parallel for reduction(+:lBondPrivate)
for(int l=0;l<(*System).getMolecule()[k].readNBond();l++)
{
//These are the first and second particles of the bond
int firstParticle=(*System).getMolecule()[k].getBonds()[l].s[0];
int secondParticle=(*System).getMolecule()[k].getBonds()[l].s[1];
//calculate bond length using minimum image
T dx=p[firstParticle].x-p[secondParticle].x;
T dy=p[firstParticle].y-p[secondParticle].y;
T dz=p[firstParticle].z-p[secondParticle].z;
if(dx>=s.x/2.0) dx-=s.x;
if(dx<=-s.x/2.0) dx+=s.x;
if(dy>=s.y/2.0) dy-=s.y;
if(dy<=-s.y/2.0) dy+=s.y;
if(dz>=s.z/2.0) dz-=s.z;
if(dz<=-s.z/2.0) dz+=s.z;
lBondPrivate+=sqrt(dx*dx+dy*dy+dz*dz);
}
lBond+=lBondPrivate;
nBond+=(*System).getMolecule()[k].readNBond();
break;
}
case BEND:
{
for(int l=0;l<(*System).getMolecule()[k].readNBond();l++)
{
//These are the first and second particles of the bond
int firstParticle=(*System).getMolecule()[k].getBonds()[l].s[0];
int secondParticle=(*System).getMolecule()[k].getBonds()[l].s[1];
int thirdParticle=(*System).getMolecule()[k].getBonds()[l].s[2];
twoVector<T> dr;
threeVector<T> da, db;
//calculate bond length using minimum image
da.x=p[firstParticle].x-p[secondParticle].x;
da.y=p[firstParticle].y-p[secondParticle].y;
da.z=p[firstParticle].z-p[secondParticle].z;
db.x=p[secondParticle].x-p[thirdParticle].x;
db.y=p[secondParticle].y-p[thirdParticle].y;
db.z=p[secondParticle].z-p[thirdParticle].z;
if(da.x>=s.x/2.0) da.x-=s.x;
if(da.x<=-s.x/2.0) da.x+=s.x;
if(da.y>=s.y/2.0) da.y-=s.y;
if(da.y<=-s.y/2.0) da.y+=s.y;
if(da.z>=s.z/2.0) da.z-=s.z;
if(da.z<=-s.z/2.0) da.z+=s.z;
if(db.x>=s.x/2.0) db.x-=s.x;
if(db.x<=-s.x/2.0) db.x+=s.x;
if(db.y>=s.y/2.0) db.y-=s.y;
if(db.y<=-s.y/2.0) db.y+=s.y;
if(db.z>=s.z/2.0) db.z-=s.z;
if(db.z<=-s.z/2.0) db.z+=s.z;
dr.s[0]=sqrt(da.x*da.x+da.y*da.y+da.z*da.z);
dr.s[1]=sqrt(db.x*db.x+db.y*db.y+db.z*db.z);
lBend.s[0]+=dr.s[0];
lBend.s[1]+=dr.s[1];
costhetaBend+=(da.x*db.x+da.y*db.y+da.z*db.z)/(dr.s[0]*dr.s[1]);
}
nBend+=(*System).getMolecule()[k].readNBond();
potential+=(*System).doBendPotential(k);
break;
}
case CHAIN:
{
potential+=(*System).doChainPotential(k);
break;
}
case BEAD:
{
T tempBeadPotential=(*System).doBeadPotential(k);
beadPotential+=tempBeadPotential;
potential+=tempBeadPotential;
nBeads++;
break;
}
case BOUNDARY:
{
potential+=(*System).doBoundaryPotential(k);
break;
}
case FLOATING_BASE:
{
potential+=(*System).doFloatingBasePotential(k);
break;
}
case ZTORQUE:
{
potential+=(*System).doZTorquePotential(k);
break;
}
case ZPOWERPOTENTIAL:
{
potential+=(*System).doZPowerPotential(k);
break;
}
case NANOCORE:
{
T tempBeadPotential=(*System).doNanoCorePotential(k);
beadPotential+=tempBeadPotential;
potential+=tempBeadPotential;
nBeads++;
break;
}
case BALL:
{
potential+=(*System).doBallPotential(k);
break;
}
default:
{
//does nothing
break;
}
}
}
std::fstream dataFile;
std::string buf("potential_");
buf+=name;
buf+=".dat";
dataFile.open(buf.c_str(), std::ios::app | std::ios::out);
dataFile << (*System).readInitialTime() << '\t' << potential << std::endl;
dataFile.close();
//Just copy this one and use it as a template