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area_and_volume.cc
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area_and_volume.cc
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//#include "network.h"
//#include <voro++.hh>
#include <sstream>
#include "area_and_volume.h"
#include "networkinfo.h"
#include "channel.h"
#include "string_additions.h"
#include "networkaccessibility.h"
#include "general.h"
#include "material.h"
using namespace std;
using namespace voro;
/** Returns the density of the provided ATOM_NETWORK, assuming it represents a single
* unit cell, in g/cm^3. */
double calcDensity(ATOM_NETWORK *atmnet){
double volume = calcDeterminant(atmnet->ucVectors); // Units of A^3
vector<ATOM>::iterator iter = atmnet->atoms.begin();
double massSum = 0;
while(iter != atmnet->atoms.end()){
massSum += iter->mass;
iter++;
}
return massSum/(AVOGRADOS_NUMBER*volume)*1.0e24; // Units of g/cm^3
}
/* Print the coordinates collected in MC sampling to the provides string
* This is the new version of the function that writes the output in all
* fromats of interests */
void NEWreportPoints(ostream &output, ATOM_NETWORK *atmnet, vector<Point> *axsPoints, vector<int> *axsPChIDs,
vector<Point> *inaxsPoints, vector<int> *inaxsPPIDs,
string type)
{
if(type=="ZEOVIS")
{
output << "{color green}" << "\n";
for(unsigned int i = 0; i < axsPoints->size(); i++){
Point coords = atmnet->abc_to_xyz(axsPoints->at(i));
output << "{point { " << coords[0] << " " << coords[1] << " " << coords[2] << "}}" << "\n";
};
output << "{color red}" << "\n";
for(unsigned int i = 0; i < inaxsPoints->size(); i++){
Point coords = atmnet->abc_to_xyz(inaxsPoints->at(i));
output << "{point {" << coords[0] << " " << coords[1] << " " << coords[2] << "}}" << "\n";
};
}
else if(type=="VISIT")
{
for(unsigned int i = 0; i < axsPoints->size(); i++){
Point coords = atmnet->abc_to_xyz(axsPoints->at(i));
output << coords[0] << " " << coords[1] << " " << coords[2] << " 1 a " << axsPChIDs->at(i) << "\n";
}
for(unsigned int i = 0; i < inaxsPoints->size(); i++){
Point coords = atmnet->abc_to_xyz(inaxsPoints->at(i));
output << coords[0] << " " << coords[1] << " " << coords[2] << " 0 n " << inaxsPPIDs->at(i) << "\n";
}
}
else if(type=="LIVERPOOL")
{
for(unsigned int i = 0; i < axsPoints->size(); i++){
Point coords = axsPoints->at(i);
output << coords[0] << " " << coords[1] << " " << coords[2] << " 1 a " << axsPChIDs->at(i) << "\n";
}
for(unsigned int i = 0; i < inaxsPoints->size(); i++){
Point coords = inaxsPoints->at(i);
output << coords[0] << " " << coords[1] << " " << coords[2] << " 0 n " << inaxsPPIDs->at(i) << "\n";
}
}
else
{
cout << "Output format unknown. Points not saved\n";
};
} //
/* Print the coordinates collected in MC sampling with additional column (value vector) to the provides string
* This is the new version of the function that writes the output in all
* fromats of interests */
void NEWreportPointsValue(ostream &output, ATOM_NETWORK *atmnet, vector<Point> *axsPoints, vector<int> *axsPChIDs,
vector<double> *value, string type)
{
if(type=="ZEOVIS")
{
cout << "ZEOVIS not supported. Not saving anything.\n";
}
else if(type=="VISIT")
{
for(unsigned int i = 0; i < axsPoints->size(); i++){
Point coords = atmnet->abc_to_xyz(axsPoints->at(i));
output << coords[0] << " " << coords[1] << " " << coords[2] << " " << axsPChIDs->at(i) << " " << value->at(i) << "\n";
}
}
else if(type=="LIVERPOOL")
{
for(unsigned int i = 0; i < axsPoints->size(); i++){
Point coords = axsPoints->at(i);
output << coords[0] << " " << coords[1] << " " << coords[2] << " " << axsPChIDs->at(i) << " " << value->at(i) << "\n";
}
}
else
{
cout << "Output format unknown. Points not saved\n";
};
} //
/* Print the coordinates contained in the provided vectors in a manner that they can be
* displayed using ZeoVis and its VMD interface. Accessible points are colored green while
* inaccessible points are colored red.*/
void reportPoints(ostream &output, vector<Point> axsPoints, vector<Point> inaxsPoints){
output << "{color green}" << "\n";
for(unsigned int i = 0; i < axsPoints.size(); i++){
Point coords = axsPoints.at(i);
output << "{point { " << coords[0] << " " << coords[1] << " " << coords[2] << "}}" << "\n";
}
output << "{color red}" << "\n";
for(unsigned int i = 0; i < inaxsPoints.size(); i++){
Point coords = inaxsPoints.at(i);
output << "{point {" << coords[0] << " " << coords[1] << " " << coords[2] << "}}" << "\n";
}
}
void reportResampledPoints(ostream &output, vector< pair<int, Point> > resampledInfo){
output << "set num_resamples " << resampledInfo.size() << "\n";
for(unsigned int i = 0; i < resampledInfo.size(); i++){
Point coords = resampledInfo[i].second;
output << "set rpoints(" << i << ") {" << coords[0] << " " << coords[1] << " " << coords[2] << "} " << "\n";
output << "set rcenters(" << i << ") " << resampledInfo[i].first << "\n";
}
}
/* Print the coordinates contained in the provided vectors in a manner that they can be
* * displayed using VisIT or analyzed using external programs using similar formating
* */
void reportPointsVisIT(ostream &output, vector<Point> axsPoints, vector<Point> inaxsPoints){
for(unsigned int i = 0; i < axsPoints.size(); i++){
Point coords = axsPoints.at(i);
output << coords[0] << " " << coords[1] << " " << coords[2] << " 1 a" << "\n";
}
for(unsigned int i = 0; i < inaxsPoints.size(); i++){
Point coords = inaxsPoints.at(i);
output << coords[0] << " " << coords[1] << " " << coords[2] << " 0 n" << "\n";
}
}
void reportPointsVisIT(ostream &output, vector<Point> axsPoints, vector<int> axsPChIDs, vector<Point> inaxsPoints, vector<int> inaxsPPIDs){
for(unsigned int i = 0; i < axsPoints.size(); i++){
Point coords = axsPoints.at(i);
output << coords[0] << " " << coords[1] << " " << coords[2] << " 1 a " << axsPChIDs[i] << "\n";
}
for(unsigned int i = 0; i < inaxsPoints.size(); i++){
Point coords = inaxsPoints.at(i);
output << coords[0] << " " << coords[1] << " " << coords[2] << " 0 n " << inaxsPPIDs[i] << "\n";
}
}
/* To adjust the sampling point to minimize its distance with the central atom, shift the point by the reverse of the
atom shift vector.
*/
void adjustSamplingPoint(Point *samplingPointXYZ, Point newAtomCoordsXYZ, Point origAtomCoordsXYZ, ATOM_NETWORK *atmnet){
Point xyzShift = origAtomCoordsXYZ.subtract(newAtomCoordsXYZ);
Point abcShift = atmnet->xyz_to_abc(xyzShift);
atmnet->translatePoint(samplingPointXYZ, abcShift[0], abcShift[1], abcShift[2]);
}
// Function defined in network.cc
void* performVoronoiDecomp(bool, ATOM_NETWORK *, VORONOI_NETWORK *, vector<VOR_CELL> &, bool, vector<BASIC_VCELL> &);
/** Returns the volume accessible to a particle of the provided radius. Accessible volume is defined as any region of space
* in which the center of the particle of the provided radius can reach. Excludes inaccessible pockets if requested */
double calcAV(ATOM_NETWORK *atmnet, ATOM_NETWORK *orgatmnet, bool highAccuracy, double r_probe_chan, double r_probe, int numSamples, bool excludePockets, ostream &output, char *filename, bool visualize, bool VisITflag, bool LiverpoolFlag, bool blockingMode, double low_dist_cutoff, double high_dist_cutoff, bool ProbeOccupiableFlag){
//determine whether we are only sampling volume within a specific distance range of the surface
bool within_range = false;
if(!(low_dist_cutoff<0 || high_dist_cutoff<0)) {
if(high_dist_cutoff<low_dist_cutoff) { //swap them
double temp = low_dist_cutoff;
low_dist_cutoff = high_dist_cutoff;
high_dist_cutoff = temp;
}
within_range = true;
}
// Create an object that handles analysis of accessibility of sampled points
AccessibilityClass accessAnalysis;
if(highAccuracy) accessAnalysis.setupAndFindChannels(atmnet, orgatmnet, highAccuracy, r_probe_chan, r_probe);
else accessAnalysis.setupAndFindChannels(atmnet, atmnet, highAccuracy, r_probe_chan, r_probe);
// setting up MC sampling
srand(randSeed);
vector<Point> axsPoints = vector<Point> (); // stores accessible points
vector<int> axsPointsChannelIDs; // stores the corresponding channel IDs
vector<Point> inaxsPoints = vector<Point> (); // inaccessible points
vector<int> inaxsPointsPocketIDs; // stores the corresponding pocket IDs
vector<Point> insidePoints = vector<Point> (); //domod: points inside atoms
vector<Point> narrowPoints = vector<Point> (); //domod: points not inside atoms, nor accessible, nor inaccessible
int count = 0;
int count_inaxs = 0;
int count_inside = 0; //domod: added to count samplepoins inside atoms
int count_within_range = 0;
int count_outside_range = 0;
vector<double> mindist_axs; // domod:
vector<double> mindist_inaxs;
// MC statistics can be collected w.r.t to identified channels and inaccessible pockets
vector<int> count_inChannel(accessAnalysis.n_channels,0);
vector<int> count_inPocket(accessAnalysis.n_pockets,0);
for(int i = 0; i < numSamples; i++){
bool overlaps = false;
bool inside = false;
double mindist_domod;
// Randomly sample point across the unit cell
double aPoint = (rand()*1.0)/RAND_MAX;
double bPoint = (rand()*1.0)/RAND_MAX;
double cPoint = (rand()*1.0)/RAND_MAX;
// Convert coords relative to the unit cell vectors into (x,y,z) coords
Point samplingPoint = atmnet->abc_to_xyz(aPoint, bPoint, cPoint);
// Calling accessibility object to determine accessibility of the point (this replaced a big chunk of code by Thomas)
pair<bool,bool> answer = (accessAnalysis.isVPointInsideAtomAndNotAccessible(samplingPoint,mindist_domod));
inside = answer.first; overlaps = answer.second;
if(accessAnalysis.needToResample() == true) i--; // the sampled point could not be analyzed in isVPointInsideAtomAndNotAccessible() function, resampling needed
if(inside == false && excludePockets == false) overlaps = false; // if ignore inacceible pockets, treat the point as accessible (unless inside atom)
//domod start: store also inside points
if(inside){
count_inside++;
Point abcCoords = Point(aPoint, bPoint, cPoint);
Point coords = atmnet->abc_to_xyz(abcCoords);
insidePoints.push_back(coords);
};
//domod end
// Store sampled points that did not overlap with an atom but were inaccessible for later visualization
if(accessAnalysis.needToResample() == false && !inside && overlaps){
mindist_inaxs.push_back(mindist_domod); //domod: store the mindistance with an atom
count_inaxs++;
pair <int,int> CoP = accessAnalysis.lastChannelOrPocket();
if(CoP.first!=-1)
{
cout << "Error: CoP.first!=-1 in pocket, consult source code provider\n";
} else {
count_inPocket[CoP.second]++;
};
if(!within_range) {
Point abcCoords = Point(aPoint, bPoint, cPoint);
Point coords = atmnet->abc_to_xyz(abcCoords);
inaxsPoints.push_back(coords);
inaxsPointsPocketIDs.push_back(CoP.second);
};
};
// Store accessible points for later visualization
if(accessAnalysis.needToResample() == false && !overlaps) {
mindist_axs.push_back(mindist_domod);
count++;
pair <int,int> CoP = accessAnalysis.lastChannelOrPocket();
if(CoP.second!=-1)
{
cout << "Error: CoP.second!=-1 in channel, consult source code provider\n";
} else {
count_inChannel[CoP.first]++;
};
Point abcCoords = Point(aPoint, bPoint, cPoint);
Point coords = atmnet->abc_to_xyz(abcCoords);
if(within_range) {
if(accessAnalysis.lastMinDist() >= low_dist_cutoff && accessAnalysis.lastMinDist() <= high_dist_cutoff) { //NOTE: minDist is the distance between centroids, it is NOT the distance to the surface - here we are comparing this distance to the tolerance range
count_within_range++;
axsPoints.push_back(coords);
} else {
count_outside_range++;
inaxsPoints.push_back(coords);
}
} else
{
axsPoints.push_back(coords);
axsPointsChannelIDs.push_back(CoP.first);
};
}
}; // ends a for loop over all sampled points
// Write the necessary commands to the output stream
// necessary to visualize the sampling
if(visualize){
if(VisITflag == false)
{
reportPoints(output, axsPoints, inaxsPoints);
}
else{
if(LiverpoolFlag == false)
{
//report points in std. VisIt format
reportPointsVisIT(output, axsPoints, inaxsPoints);
}
else{
//report points in Liverpool format
vector<Point> LiverpoolAxsPoints = vector<Point> ();
vector<Point> LiverpoolInaxsPoints = vector<Point> ();
for(unsigned i = 0; i < axsPoints.size(); i++)
{
LiverpoolAxsPoints.push_back(atmnet->xyz_to_abc(axsPoints[i]));
};
for(unsigned j = 0; j < inaxsPoints.size(); j++)
{
LiverpoolInaxsPoints.push_back(atmnet->xyz_to_abc(inaxsPoints[j]));
};
if(within_range == true) reportPointsVisIT(output, LiverpoolAxsPoints, LiverpoolInaxsPoints);
else reportPointsVisIT(output, LiverpoolAxsPoints, axsPointsChannelIDs, LiverpoolInaxsPoints, inaxsPointsPocketIDs);
};
};
//reportResampledPoints(output, resampledInfo);
}
// Write blocknig spheres based on current sampling points if blocking routine
// has been requested
if(blockingMode)
{
//report points in fractonal coordinates (Liverpool format used in visualization)
vector<Point> LiverpoolAxsPoints = vector<Point> ();
vector<Point> LiverpoolInaxsPoints = vector<Point> ();
for(unsigned i = 0; i < axsPoints.size(); i++)
{
LiverpoolAxsPoints.push_back(atmnet->xyz_to_abc(axsPoints[i]));
};
for(unsigned j = 0; j < inaxsPoints.size(); j++)
{
LiverpoolInaxsPoints.push_back(atmnet->xyz_to_abc(inaxsPoints[j]));
};
// call this if arg are point in factional coordiantes
blockPockets(atmnet, output, LiverpoolAxsPoints, axsPointsChannelIDs, LiverpoolInaxsPoints, inaxsPointsPocketIDs, r_probe_chan);
//call this if Cartesian points are to be used
// blockPockets(atmnet, output, axsPoints, axsPointsChannelIDs, inaxsPoints, inaxsPointsPocketIDs, r_probe_chan);
};
// Warn user if points were resampled
int resampleCount = accessAnalysis.getResampleCount();
if(resampleCount != 0){
cerr << "\n" << "\n"
<< "Warning: Resampled " << resampleCount << " points out of " << numSamples
<< " when analyzing " << atmnet->name << "\n"
<< "\n" << "\n";
}
//domod start: Further calculation of probe occupiable volume
//
//
int count_domod, count_domod_inaxs, count_domod_inside, count_domod_narrow;
if(ProbeOccupiableFlag == true)
{
count_domod = count; //points in the big accessible volume = points in the small accessible volume
count_domod_inaxs = count_inaxs; //points in the big inaccessible volume = points in the small inaccessible volume
count_domod_inside = count_inside; //points inside atoms = points outside small volumes
count_domod_narrow = 0; //points in a narrow inaccessible volume
if (r_probe > 0.0)
{
bool alreadyfound = false;
printf("ProbeOccupiableLoopStart: atoms: %d count: %d count_inaxs: %d count_inside: %d count_narrow: %d\n",
orgatmnet->numAtoms, count_domod, count_domod_inaxs, count_domod_inside, count_domod_narrow); //domodebug
//printf("DOMODEBUG domod loop \n"); //domodebug
//printf("%f %f %f %f %f %f %f %f %f\n",orgatmnet->ucVectors[0][0],orgatmnet->ucVectors[0][1],orgatmnet->ucVectors[0][2],
// orgatmnet->ucVectors[1][0],orgatmnet->ucVectors[1][1],orgatmnet->ucVectors[1][2],
// orgatmnet->ucVectors[2][0],orgatmnet->ucVectors[2][1],orgatmnet->ucVectors[2][2]);
for (int i=0; i<count_inside; i++)
{
alreadyfound=false;
//first make a loop to check again easily if the sample point is close to an atom:
//it is faster because we have less atoms than sample points and we discard all the "really inside" points
//!!! The purpose of the first loop is only to speed up the calculation to avoid the loop with all the in/accessible points in the small volume
for (int j=0; j<(orgatmnet->numAtoms); j++) //LOOP1: check if it is close to an atom.
{
ATOM curAtom = orgatmnet->atoms[j];
double minDist = orgatmnet->calcDistanceXYZ(
insidePoints[i][0],
insidePoints[i][1],
insidePoints[i][2],
curAtom.x,
curAtom.y,
curAtom.z);
//printf("%d %d |samplepoint: %6.3f %6.3f %6.3f |atom: %6.3f %6.3f %6.3f |dist: %6.3f |rad: %6.3f\n", i,j,insidePoints[i][0],insidePoints[i][1],insidePoints[i][2],curAtom.x,curAtom.y,curAtom.z,minDist,curAtom.radius); //domodebug
if (minDist <= curAtom.radius)
{
//keep it in count_inside
alreadyfound=true;
//printf("DOMODEBUG inside |samplepoint: %6.3f %6.3f %6.3f\n",insidePoints[i][0],insidePoints[i][1],insidePoints[i][2]); //domodebug
break;
}
}
if (!alreadyfound)
{
for (int j=0; j<count; j++) //LOOP2: check if it is close to an accessible point
{
double minDist = orgatmnet->calcDistanceXYZ(
insidePoints[i][0],
insidePoints[i][1],
insidePoints[i][2],
axsPoints[j][0],
axsPoints[j][1],
axsPoints[j][2]);
//if (minDist <= rprobe) //domodold
if (minDist <= r_probe+mindist_axs[j]) //domod: test with r_probe+delta with delta=mindist-r_probe
{
axsPoints.push_back(insidePoints[i]); //domodcheck: I don't want to touch this: maybe it is used for other calculations!
count_domod_inside--;
count_domod++;
alreadyfound=true;
//printf("DOMODEBUG axs |samplepoint: %6.3f %6.3f %6.3f\n",insidePoints[i][0],insidePoints[i][1],insidePoints[i][2]); //domodebug
break;
}
}
}
if (!alreadyfound)
{
for (int j=0; j<count_inaxs; j++) //LOOP3: check if it is close to an inaccessible point (NB: accessible point have priority in case of they are both in an accessible and non accessible volume)
{
double minDist = orgatmnet->calcDistanceXYZ(
insidePoints[i][0],
insidePoints[i][1],
insidePoints[i][2],
inaxsPoints[j][0],
inaxsPoints[j][1],
inaxsPoints[j][2]);
//if (minDist <= rprobe) //domodold
if (minDist <= r_probe+mindist_inaxs[j]) //domod: test with r_probe+delta with delta=mindist-r_probe
{
inaxsPoints.push_back(insidePoints[i]);
count_domod_inside--;
count_domod_inaxs++;
alreadyfound=true;
//printf("DOMODEBUG inax \n"); //domodebug
break;
}
}
}
if (!alreadyfound)
{
narrowPoints.push_back(insidePoints[i]);
//narrowPoints[count_domod_narrow][1]=insidePoints[i][1];
//narrowPoints[count_domod_narrow][2]=insidePoints[i][2];
count_domod_inside--;
count_domod_narrow++;
//printf("DOMODEBUG narrow |samplepoint: %6.3f %6.3f %6.3f\n",insidePoints[i][0],insidePoints[i][1],insidePoints[i][2]); //domodebug
}
}
printf("ProbeOccupiableLoopEnd: atoms: %d count: %d count_inaxs: %d count_inside: %d count_narrow: %d\n",
orgatmnet->numAtoms, count_domod, count_domod_inaxs, count_domod_inside, count_domod_narrow); //domodebug
}
//domod end
/*domodprintxyz: print a .xyz with points-- */
/*
ofstream myfile;
myfile.open ("see_access.xyz");
myfile << count_domod+(orgatmnet->numAtoms) << "\n";
myfile << "CELL: " << orgatmnet->a << " " << orgatmnet->b << " " << orgatmnet->c << " " << orgatmnet->alpha << " " << orgatmnet->beta << " " << orgatmnet->gamma << " #accessible points\n";
for (int i=0; i<count_domod; i++) {
if (i<count)
myfile << "He " << axsPoints[i][0] << " " << axsPoints[i][1] << " " << axsPoints[i][2] << "\n"; //before
else
myfile << "Ne " << axsPoints[i][0] << " " << axsPoints[i][1] << " " << axsPoints[i][2] << "\n"; //after
}
for (int i=0; i<orgatmnet->numAtoms; i++) {
ATOM curAtom = orgatmnet->atoms[i];
myfile << curAtom.type << " " << curAtom.x << " " << curAtom.y << " " << curAtom.z << "\n";
}
myfile.close();
//-------------------------------------
myfile.open ("see_nonaccess.xyz");
myfile << count_domod_inaxs+(orgatmnet->numAtoms) << "\n";
myfile << "CELL: " << orgatmnet->a << " " << orgatmnet->b << " " << orgatmnet->c << " " << orgatmnet->alpha << " " << orgatmnet->beta << " " << orgatmnet->gamma << " #non accessible points\n";
for (int i=0; i<count_domod_inaxs; i++) {
if (i<count_inaxs)
myfile << "He " << inaxsPoints[i][0] << " " << inaxsPoints[i][1] << " " << inaxsPoints[i][2] << "\n"; //before
else
myfile << "Ne " << inaxsPoints[i][0] << " " << inaxsPoints[i][1] << " " << inaxsPoints[i][2] << "\n"; //after
}
for (int i=0; i<orgatmnet->numAtoms; i++) {
ATOM curAtom = orgatmnet->atoms[i];
myfile << curAtom.type << " " << curAtom.x << " " << curAtom.y << " " << curAtom.z << "\n";
}
myfile.close();
//--------------------------------------
myfile.open ("see_narrow.xyz");
myfile << count_domod_narrow+(orgatmnet->numAtoms) << "\n";
myfile << "CELL: " << orgatmnet->a << " " << orgatmnet->b << " " << orgatmnet->c << " " << orgatmnet->alpha << " " << orgatmnet->beta << " " << orgatmnet->gamma << " #narrow points\n";
for (int i=0; i<count_domod_narrow; i++) {
myfile << "He " << narrowPoints[i][0] << " " << narrowPoints[i][1] << " " << narrowPoints[i][2] << "\n";
}
for (int i=0; i<orgatmnet->numAtoms; i++) {
ATOM curAtom = orgatmnet->atoms[i];
myfile << curAtom.type << " " << curAtom.x << " " << curAtom.y << " " << curAtom.z << "\n";
}
myfile.close();
//--------------------------------------
myfile.open ("see_cluster.xyz");
myfile << atmnet->numAtoms << "\n";
myfile << "CELL: " << orgatmnet->a << " " << orgatmnet->b << " " << orgatmnet->c << " " << orgatmnet->alpha << " " << orgatmnet->beta << " " << orgatmnet->gamma << " #cluster atoms after moltiplication + radius\n";
for (int i=0; i<atmnet->numAtoms; i++) {
ATOM curAtom = atmnet->atoms[i];
myfile << curAtom.type << " " << curAtom.x << " " << curAtom.y << " " << curAtom.z << " " << curAtom.radius << "\n";
}
myfile.close();
//-------------------------------------
myfile.open ("see_all.xyz");
myfile << count_domod+count_domod_inaxs+count_domod_narrow+(orgatmnet->numAtoms) << "\n";
myfile << "CELL: " << orgatmnet->a << " " << orgatmnet->b << " " << orgatmnet->c << " " << orgatmnet->alpha << " " << orgatmnet->beta << " " << orgatmnet->gamma
<< " #He: AX_before, Ne: AX_after, Ar: NAX_before, Kr: NAX_after, Xe: narrow\n";
for (int i=0; i<count_domod; i++) {
if (i<count)
myfile << "He " << axsPoints[i][0] << " " << axsPoints[i][1] << " " << axsPoints[i][2] << "\n";
else
myfile << "Ne " << axsPoints[i][0] << " " << axsPoints[i][1] << " " << axsPoints[i][2] << "\n";
}
for (int i=0; i<count_domod_inaxs; i++) {
if (i<count_inaxs)
myfile << "Ar " << inaxsPoints[i][0] << " " << inaxsPoints[i][1] << " " << inaxsPoints[i][2] << "\n";
else
myfile << "Kr " << inaxsPoints[i][0] << " " << inaxsPoints[i][1] << " " << inaxsPoints[i][2] << "\n";
}
for (int i=0; i<count_domod_narrow; i++) {
myfile << "Xe " << narrowPoints[i][0] << " " << narrowPoints[i][1] << " " << narrowPoints[i][2] << "\n";
}
for (int i=0; i<orgatmnet->numAtoms; i++) {
ATOM curAtom = orgatmnet->atoms[i];
myfile << curAtom.type << " " << curAtom.x << " " << curAtom.y << " " << curAtom.z << "\n";
}
myfile.close();
*/
/* end domodprintxyz------------------*/
}; // Ends If(ProbeOccupiableflag = true)
// Final analysis
double volumeFraction, origVolume, av;
if(ProbeOccupiableFlag == false)
{
volumeFraction = count*1.0/numSamples;
origVolume = calcDeterminant(atmnet->ucVectors);
av = volumeFraction * origVolume;
// Write the results to the output stream
if(!visualize&&!blockingMode){
double volumeFraction_inaxs = count_inaxs*1.0/numSamples;
double rho_crystal = calcDensity(atmnet);
double avPerMass = volumeFraction/rho_crystal;
double av_inaxs = volumeFraction_inaxs * origVolume;
double avPerMass_inaxs = volumeFraction_inaxs/rho_crystal;
// output << newAtomNet.name << " ";
output << "@ " << filename << " ";
output << "Unitcell_volume: " << origVolume << " Density: " << rho_crystal << " ";
output << "AV_A^3: " << av << " "
<< "AV_Volume_fraction: " << volumeFraction << " "
<< "AV_cm^3/g: " << avPerMass << " "
<< "NAV_A^3: " << av_inaxs << " "
<< "NAV_Volume_fraction: " << volumeFraction_inaxs << " "
<< "NAV_cm^3/g: " << avPerMass_inaxs;
if(within_range) {
double volumeFraction_within_range = count_within_range*1.0/numSamples;
double av_within_range = volumeFraction_within_range * origVolume;
double avPerMass_within_range = volumeFraction_within_range/rho_crystal;
output << " range_A^3: " << av_within_range << " "
<< "range_Volume_fraction: " << volumeFraction_within_range << " "
<< "range_cm^3/g: " << avPerMass_within_range;
}
output << "\n";
output << "Number_of_channels: " << count_inChannel.size() << " Channel_volume_A^3: ";
for(unsigned int i = 0; i < count_inChannel.size(); i++)
{
// output << count_inChannel[i]*100.00/count << " ";
output << count_inChannel[i]*(1.0/numSamples) * origVolume << " ";
};
output << "\nNumber_of_pockets: " << count_inPocket.size() << " Pocket_volume_A^3: ";
for(unsigned int i = 0; i < count_inPocket.size(); i++)
{
// output << count_inPocket[i]*100.00/count_inaxs << " ";
output << count_inPocket[i]*(1.0/numSamples) * origVolume << " ";
};
output << "\n";
} // ends "if(!visualize){..." writing output
} else { // Different printout in case of probe occupiable calcluation
volumeFraction = count_domod*1.0/numSamples; //domodinfo: here is the value for accessible points
origVolume = calcDeterminant(atmnet->ucVectors);
av = volumeFraction * origVolume;
// Write the results to the output stream
if(!visualize&&!blockingMode){
double volumeFraction_inaxs = count_domod_inaxs*1.0/numSamples; //domodinfo: here is the value for non accessible points
double rho_crystal = calcDensity(atmnet);
double avPerMass = volumeFraction/rho_crystal;
double av_inaxs = volumeFraction_inaxs * origVolume;
double avPerMass_inaxs = volumeFraction_inaxs/rho_crystal;
// output << newAtomNet.name << " ";
output << "@ " << filename << " ";
output << "Unitcell_volume: " << origVolume << " Density: " << rho_crystal << " ";
output << "POAV_A^3: " << av << " "
<< "POAV_Volume_fraction: " << volumeFraction << " "
<< "POAV_cm^3/g: " << avPerMass << " "
<< "PONAV_A^3: " << av_inaxs << " "
<< "PONAV_Volume_fraction: " << volumeFraction_inaxs << " "
<< "PONAV_cm^3/g: " << avPerMass_inaxs;
output << "\n";
output << "PROBE_OCCUPIABLE_VOL_CALC: filename| density(g/cm3)| probe rad| N points| probe ctr A fract| probe ctr NA fract| A fract| NA fract| narrow fract |ovlp fract.\n";
output << "PROBE_OCCUPIABLE___RESULT: "
<< filename << "\t"
<< rho_crystal << "\t"
<< r_probe << "\t"
<< numSamples << "\t"
<< (double)count/(double)numSamples << "\t"
<< (double)count_inaxs/(double)numSamples << "\t"
<< (double)count_domod/(double)numSamples << "\t"
<< (double)count_domod_inaxs/(double)numSamples << "\t"
<< (double)count_domod_narrow/(double)numSamples << "\t"
<< (double)count_domod_inside/(double)numSamples << "\n";
} // ends "if(!visualize){..." writing output
}; // ends else () when ProbeOccupiableFlag == true
accessAnalysis.deconstruct();
return av;
}
/** NEWcalcAV is operating on Material class. It does not have any output savings routines */
double NEWcalcAV(MATERIAL *Mat, double r_probe, int numSamples){
return NEWcalcAV(Mat, r_probe, numSamples, -1, -1);
}
/** NEWcalcAV is operating on Material class. It does not have any output savings routines */
double NEWcalcAV(MATERIAL *Mat, double r_probe, int numSamples, double low_dist_cutoff, double high_dist_cutoff){
// Inital checks
if(!(Mat->accessAnalysis.alreadySegmentedFlag))
{
cerr << "Cannot run calcAV without prior accessibility analysis.\nExiting with return 0\n";
return 0;
}
// Setting parameters
Mat->AVprobeRadius = r_probe;
// Cleaning structures in case of previous runs
Mat->AVcount = 0;
Mat->AVcount_inaxs = 0;
Mat->AVcount_within_range = 0;
Mat->AVcount_outside_range = 0;
Mat->AVaxsPoints.clear();
Mat->AVaxsPointsChannelIDs.clear();
Mat->AVinaxsPoints.clear();
Mat->AVinaxsPointsPocketIDs.clear();
Mat->AVcount_inChannel.clear();
Mat->AVcount_inPocket.clear();
//determine whether we are only sampling volume within a specific distance range of the surface
bool within_range = false;
if(!(low_dist_cutoff<0 || high_dist_cutoff<0)) {
if(high_dist_cutoff<low_dist_cutoff) { //swap them
double temp = low_dist_cutoff;
low_dist_cutoff = high_dist_cutoff;
high_dist_cutoff = temp;
}
within_range = true;
}
Mat->AVwithin_rangeFlag = within_range;
// setting up MC sampling
srand(randSeed);
numSamples = int(numSamples * calcDeterminant(Mat->atmnet.ucVectors));
Mat->AVnumSamples = numSamples;
cout << "Number of samples in volume calc: " << numSamples << endl;
bool excludePockets = true; // this is default (in old version, without voro-stuff it was used)
int count = 0;
int count_inaxs = 0;
int count_within_range = 0;
int count_outside_range = 0;
// MC statistics can be collected w.r.t to identified channels and inaccessible pockets
Mat->AVcount_inChannel.resize(Mat->accessAnalysis.n_channels,0);
Mat->AVcount_inPocket.resize(Mat->accessAnalysis.n_pockets,0);
for(int i = 0; i < numSamples; i++){
bool overlaps = false;
bool inside = false;
// Randomly sample point across the unit cell
double aPoint = (rand()*1.0)/RAND_MAX;
double bPoint = (rand()*1.0)/RAND_MAX;
double cPoint = (rand()*1.0)/RAND_MAX;
// Convert coords relative to the unit cell vectors into (x,y,z) coords
Point samplingPoint = Mat->atmnet.abc_to_xyz(aPoint, bPoint, cPoint);
// Calling accessibility object to determine accessibility of the point (this replaced a big chunk of code by Thomas)
pair<bool,bool> answer = (Mat->accessAnalysis.isVPointInsideAtomAndNotAccessible(samplingPoint));
inside = answer.first; overlaps = answer.second;
if(Mat->accessAnalysis.needToResample() == true) i--; // the sampled point could not be analyzed in isVPointInsideAtomAndNotAccessible() function, resampling needed
if(inside == false && excludePockets == false) overlaps = false; // if ignore inacceible pockets, treat the point as accessible (unless inside atom)
// Store sampled points that did not overlap with an atom but were inaccessible for later visualization
if(Mat->accessAnalysis.needToResample() == false && !inside && overlaps){
count_inaxs++;
pair <int,int> CoP = Mat->accessAnalysis.lastChannelOrPocket();
if(CoP.first!=-1)
{
cout << "Error: CoP.first!=-1 in pocket, consult source code provider\n";
} else {
Mat->AVcount_inPocket[CoP.second]++;
};
if(!within_range) {
//Point abcCoords = Point(aPoint, bPoint, cPoint); // to be removed as now we store fractional coordinates
//Point coords = Mat->atmnet.abc_to_xyz(abcCoords);
Point coords = Point(aPoint, bPoint, cPoint);
Mat->AVinaxsPoints.push_back(coords);
Mat->AVinaxsPointsPocketIDs.push_back(CoP.second);
};
};
// Store accessible points for later visualization
if(Mat->accessAnalysis.needToResample() == false && !overlaps) {
count++;
pair <int,int> CoP = Mat->accessAnalysis.lastChannelOrPocket();
if(CoP.second!=-1)
{
cout << "Error: CoP.second!=-1 in channel, consult source code provider\n";
} else {
Mat->AVcount_inChannel[CoP.first]++;
};
//Point abcCoords = Point(aPoint, bPoint, cPoint); // to be removed as now we store fractional coordinates
//Point coords = Mat->atmnet.abc_to_xyz(abcCoords);
Point coords = Point(aPoint, bPoint, cPoint);
if(within_range) {
if(Mat->accessAnalysis.lastMinDist() >= low_dist_cutoff && Mat->accessAnalysis.lastMinDist() <= high_dist_cutoff) { //NOTE: minDist is the distance between centroids, it is NOT the distance to the surface - here we are comparing this distance to the tolerance range
// RECHECK IF STILL TRUE FOR NON INFLATED ATOMS
count_within_range++;
Mat->AVaxsPoints.push_back(coords);
} else {
count_outside_range++;
Mat->AVinaxsPoints.push_back(coords);
}
} else
{
Mat->AVaxsPoints.push_back(coords);
Mat->AVaxsPointsChannelIDs.push_back(CoP.first);
};
}
}; // ends a for loop over all sampled points
// Warn user if points were resampled
int resampleCount = Mat->accessAnalysis.getResampleCount();
if(resampleCount != 0){
cerr << "\n" << "\n"
<< "Warning: Resampled " << resampleCount << " points out of " << numSamples
<< " when analyzing " << Mat->atmnet.name << "\n"
<< "\n" << "\n";
};
Mat->AVcount = count;
Mat->AVcount_inaxs = count_inaxs;
Mat->AVcount_within_range = count_within_range;
Mat->AVcount_outside_range = count_outside_range;
return count/numSamples;
} // ends NEWcalcAV
/* framgents of calcAV for saving outputs
// Write the necessary commands to the output stream
// necessary to visualize the sampling
if(visualize){
if(VisITflag == false)
{
reportPoints(output, axsPoints, inaxsPoints);
}
else{
if(LiverpoolFlag == false)
{
//report points in std. VisIt format
reportPointsVisIT(output, axsPoints, inaxsPoints);
}
else{
//report points in Liverpool format
vector<Point> LiverpoolAxsPoints = vector<Point> ();
vector<Point> LiverpoolInaxsPoints = vector<Point> ();
for(unsigned i = 0; i < axsPoints.size(); i++)
{
LiverpoolAxsPoints.push_back(atmnet->xyz_to_abc(axsPoints[i]));
};
for(unsigned j = 0; j < inaxsPoints.size(); j++)
{
LiverpoolInaxsPoints.push_back(atmnet->xyz_to_abc(inaxsPoints[j]));
};
if(within_range == true) reportPointsVisIT(output, LiverpoolAxsPoints, LiverpoolInaxsPoints);
else reportPointsVisIT(output, LiverpoolAxsPoints, axsPointsChannelIDs, LiverpoolInaxsPoints, inaxsPointsPocketIDs);
};
};
//reportResampledPoints(output, resampledInfo);
}
// Write blocknig spheres based on current sampling points if blocking routine
// has been requested
if(blockingMode)
{
//report points in fractonal coordinates (Liverpool format used in visualization)
vector<Point> LiverpoolAxsPoints = vector<Point> ();
vector<Point> LiverpoolInaxsPoints = vector<Point> ();
for(unsigned i = 0; i < axsPoints.size(); i++)
{
LiverpoolAxsPoints.push_back(atmnet->xyz_to_abc(axsPoints[i]));
};
for(unsigned j = 0; j < inaxsPoints.size(); j++)
{
LiverpoolInaxsPoints.push_back(atmnet->xyz_to_abc(inaxsPoints[j]));
};
// call this if arg are point in factional coordiantes
blockPockets(atmnet, output, LiverpoolAxsPoints, axsPointsChannelIDs, LiverpoolInaxsPoints, inaxsPointsPocketIDs, r_probe_chan);
//call this if Cartesian points are to be used
// blockPockets(atmnet, output, axsPoints, axsPointsChannelIDs, inaxsPoints, inaxsPointsPocketIDs, r_probe_chan);
};
*/
/* Function that calculates and print summary of NEWcalcAV */
void NEWcalcAVprint(MATERIAL *Mat, ostream &output, char *filename) {
double volumeFraction = Mat->AVcount*1.0/Mat->AVnumSamples;
double origVolume = calcDeterminant(Mat->atmnet.ucVectors);
double av = volumeFraction * origVolume;
// Write the results to the output stream
double volumeFraction_inaxs = Mat->AVcount_inaxs*1.0/Mat->AVnumSamples;
double rho_crystal = calcDensity(&(Mat->atmnet));
double avPerMass = volumeFraction/rho_crystal;
double av_inaxs = volumeFraction_inaxs * origVolume;
double avPerMass_inaxs = volumeFraction_inaxs/rho_crystal;
// output << newAtomNet.name << " ";
output << "@ " << filename << " ";
output << "Unitcell_volume: " << origVolume << " Density: " << rho_crystal << " ";
output << "AV_A^3: " << av << " "
<< "AV_Volume_fraction: " << volumeFraction << " "
<< "AV_cm^3/g: " << avPerMass << " "
<< "NAV_A^3: " << av_inaxs << " "
<< "NAV_Volume_fraction: " << volumeFraction_inaxs << " "
<< "NAV_cm^3/g: " << avPerMass_inaxs;
if(Mat->AVwithin_rangeFlag) {
double volumeFraction_within_range = Mat->AVcount_within_range*1.0/Mat->AVnumSamples;
double av_within_range = volumeFraction_within_range * origVolume;
double avPerMass_within_range = volumeFraction_within_range/rho_crystal;
output << " range_A^3: " << av_within_range << " "
<< "range_Volume_fraction: " << volumeFraction_within_range << " "
<< "range_cm^3/g: " << avPerMass_within_range;
}
output << "\n";
output << "Number_of_channels: " << Mat->AVcount_inChannel.size() << " Channel_volume_A^3: ";
for(unsigned int i = 0; i < Mat->AVcount_inChannel.size(); i++)
{
output << Mat->AVcount_inChannel[i]*(1.0/Mat->AVnumSamples) * origVolume << " ";
};
output << "\nNumber_of_pockets: " << Mat->AVcount_inPocket.size() << " Pocket_volume_A^3: ";
for(unsigned int i = 0; i < Mat->AVcount_inPocket.size(); i++)
{
output << Mat->AVcount_inPocket[i]*(1.0/Mat->AVnumSamples) * origVolume << " ";
};
output << "\n";
}
/* backup of AV function
double calcAV(ATOM_NETWORK *atmnet, ATOM_NETWORK *orgatmnet, bool highAccuracy, double r_probe_chan, double r_probe, int numSamples, bool excludePockets, ostream &output, char *filename, bool visualize, bool VisITflag, bool LiverpoolFlag, double low_dist_cutoff, double high_dist_cutoff){
//determine whether we are only sampling volume within a specific distance range of the surface
bool within_range = false;
if(!(low_dist_cutoff<0 || high_dist_cutoff<0)) {
if(high_dist_cutoff<low_dist_cutoff) { //swap them
double temp = low_dist_cutoff;
low_dist_cutoff = high_dist_cutoff;
high_dist_cutoff = temp;
}
within_range = true;
}
// Create a temporary copy of the atomic network in which each atom's radius has been increased by the probe radius
ATOM_NETWORK newAtomNet;
atmnet->copy(&newAtomNet);
for(int i = 0; i < newAtomNet.numAtoms; i++){ newAtomNet.atoms[i].radius += r_probe; }
// Calculate and store the Voronoi network for this new atomic network
VORONOI_NETWORK vornet;
vector<BASIC_VCELL> vorcells;