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Commit 4a123b50 authored by David Rohr's avatar David Rohr
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merge with devel branch

parents 89cc32a4 9582b044
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CMakeLists.txt
View file @ 4a123b50
......@@ -11,7 +11,7 @@ FIND_PACKAGE(PkgConfig REQUIRED)
PKG_CHECK_MODULES(FFTW fftw3 REQUIRED)
INCLUDE_DIRECTORIES(${FFTW_INCLUDE_DIRS})
FIND_PACKAGE(Boost 1.54 REQUIRED)
FIND_PACKAGE(Boost 1.43 REQUIRED)
INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
FIND_PACKAGE(OpenMP)
......
bioem.cpp 100644 → 100755
View file @ 4a123b50
......@@ -57,6 +57,8 @@ int bioem::configure(int ac, char* av[])
param.writeAngles = false;
param.dumpMap = false;
param.loadMap = false;
RefMap.readMRC = false;
RefMap.readMultMRC = false;
// *************************************************************************************
cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
......@@ -66,21 +68,26 @@ int bioem::configure(int ac, char* av[])
try {
po::options_description desc("Command line inputs");
desc.add_options()
("Inputfile", po::value<std::string>(), "Name of input parameter file")
("Modelfile", po::value< std::string>() , "Name of model file")
("Particlesfile", po::value< std::string>(), "Name of paricles file")
("ReadPDB", "(Optional) If reading model file in PDB format")
("DumpMaps", "(Optional) Dump maps after they were red from maps file")
("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
("help", "(Optional) Produce help message")
;
desc.add_options()
("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
("ReadPDB", "(Optional) If reading model file in PDB format")
("ReadMRC", "(Optional) If reading particle file in MRC format")
("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
("DumpMaps", "(Optional) Dump maps after they were red from maps file")
("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
("help", "(Optional) Produce help message")
;
po::positional_options_description p;
p.add("Inputfile", -1);
p.add("Modelfile", -1);
p.add("Particlesfile", -1);
p.add("ReadPDB", -1);
p.add("ReadMRC", -1);
p.add("ReadMultipleMRC", -1);
p.add("DumpMaps", -1);
p.add("LoadMapDump", -1);
......@@ -118,6 +125,18 @@ int bioem::configure(int ac, char* av[])
Model.readPDB = true;
}
if (vm.count("ReadMRC"))
{
cout << "Reading particle file in MRC format.\n";
RefMap.readMRC=true;
}
if (vm.count("ReadMultipleMRC"))
{
cout << "Reading Multiple MRCs.\n";
RefMap.readMultMRC=true;
}
if (vm.count("DumpMaps"))
{
cout << "Dumping Maps after reading from file.\n";
......@@ -360,8 +379,11 @@ int bioem::run()
int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
{
//***************************************************************************************
//***** BioEM routine for comparing reference maps to convoluted maps *****
if (FFTAlgo)
{
//With FFT Algorithm
#pragma omp parallel for
for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
......@@ -371,6 +393,7 @@ int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, myc
}
else
{
//Without FFT Algorithm
#pragma omp parallel for
for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
......@@ -382,6 +405,9 @@ int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, myc
inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC)
{
//***************************************************************************************
//***** Calculating cross correlation in FFTALGOrithm *****
const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
{
......
include/map.h 100644 → 100755
View file @ 4a123b50
......@@ -34,8 +34,17 @@ public:
int precalculate(bioem_param& param, bioem& bio);
int PreCalculateMapsFFT(bioem_param& param);
int read_int(int *currlong, FILE *fin, int swap);
int read_float(float *currfloat, FILE *fin, int swap);
int read_float_empty (FILE *fin);
int read_char_float (float *currfloat, FILE *fin) ;
int test_mrc (const char *vol_file, int swap);
int read_MRC(const char* filename,bioem_param& param);
mycomplex_t* RefMapsFFT;
bool readMRC,readMultMRC;
int ntotRefMap;
int numPixels;
int refMapSize;
......
map.cpp 100644 → 100755
View file @ 4a123b50
......@@ -33,9 +33,56 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
fread(maps, sizeof(myfloat_t) * refMapSize, ntotRefMap, fp);
fclose(fp);
cout << "Particle Maps read from Map Dump \nTotal Number of particles: " << ntotRefMap ;
cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Particle Maps read from Map Dump\n";
}
else if(readMRC)
{
ntotRefMap=0;
if(readMultMRC)
{
ifstream input(filemap);
if (!input.good())
{
cout << "Failed to open file contaning MRC names: " << filemap << "\n";
exit(0);
}
char line[512] = {0};
char mapname[100];
char tmpm[10] = {0};
const char* indifile;
while (!input.eof())
{
input.getline(line,512);
char tmpVals[100] = {' '};
strncpy (tmpVals,line,100);
sscanf (tmpVals,"%99c",mapname);
// Check for last line
strncpy (tmpm,mapname,3);
if(strcmp(tmpm,"XXX")!=0)
{
indifile = mapname;
//Reading Multiple MRC
read_MRC(indifile,param);
}
for(int i=0;i<3;i++)mapname[i] = 'X';
for(int i=3;i<100;i++)mapname[i] = {0};
}
cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
} else {
read_MRC(filemap,param);
cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
}
}
else
{
int nummap = -1;
......@@ -113,8 +160,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
cout << ".";
ntotRefMap = nummap + 1;
maps = (myfloat_t*) reallocchk(maps, refMapSize * sizeof(myfloat_t) * ntotRefMap);
cout << "Particle Maps read from Standard File \nTotal Number of particles: " << ntotRefMap ;
cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Particle Maps read from Standard File \n";
if (param.dumpMap)
{
......@@ -130,6 +176,9 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
}
}
cout << "Total Number of particles: " << ntotRefMap;
cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
sum_RefMap = (myfloat_t*) mallocchk(sizeof(myfloat_t) * ntotRefMap);
sumsquare_RefMap = (myfloat_t*) mallocchk(sizeof(myfloat_t) * ntotRefMap);
......@@ -215,3 +264,267 @@ void bioem_Probability::init(size_t maps, size_t angles, bioem& bio)
ptr = bio.malloc_device_host(get_size(maps, angles));
set_pointers();
}
int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
{
myfloat_t st,st2;
unsigned long count;
FILE *fin;
float currfloat;
int nc, nr, ns, swap, header_ok = 1;
float xlen, ylen, zlen;
int mode, ncstart, nrstart, nsstart, ispg, nsymbt, lskflg;
float a_tmp, b_tmp, g_tmp;
int mx, my, mz,mapc, mapr, maps;
float dmin, dmax, dmean;
int n_range_viol0, n_range_viol1;
fin = fopen(filename, "rb");
if( fin == NULL ) {
cout << "ERROR opening MRC: " << filename;
exit(1);
}
n_range_viol0 = test_mrc(filename,0);
n_range_viol1 = test_mrc(filename,1);
if (n_range_viol0 < n_range_viol1) { //* guess endianism
swap = 0;
if (n_range_viol0 > 0) {
printf(" Warning: %i header field range violations detected in file %s \n", n_range_viol0,filename);
}
} else {
swap = 1;
if (n_range_viol1 > 0) {
printf("Warning: %i header field range violations detected in file %s \n", n_range_viol1,filename);
}
}
printf("\n+++++++++++++++++++++++++++++++++++++++++++\n");
printf("Reading Information from MRC: %s \n", filename);
header_ok *= read_int(&nc,fin,swap);
header_ok *= read_int(&nr,fin,swap);
header_ok *= read_int(&ns,fin,swap);
header_ok *= read_int(&mode,fin,swap);
header_ok *= read_int(&ncstart,fin,swap);
header_ok *= read_int(&nrstart,fin,swap);
header_ok *= read_int(&nsstart,fin,swap);
header_ok *= read_int(&mx,fin,swap);
header_ok *= read_int(&my,fin,swap);
header_ok *= read_int(&mz,fin,swap);
header_ok *= read_float(&xlen,fin,swap);
header_ok *= read_float(&ylen,fin,swap);
header_ok *= read_float(&zlen,fin,swap);
header_ok *= read_float(&a_tmp,fin,swap);
header_ok *= read_float(&b_tmp,fin,swap);
header_ok *= read_float(&g_tmp,fin,swap);
header_ok *= read_int(&mapc,fin,swap);
header_ok *= read_int(&mapr,fin,swap);
header_ok *= read_int(&maps,fin,swap);
header_ok *= read_float(&dmin,fin,swap);
header_ok *= read_float(&dmax,fin,swap);
header_ok *= read_float(&dmean,fin,swap);
header_ok *= read_int(&ispg,fin,swap);
header_ok *= read_int(&nsymbt,fin,swap);
header_ok *= read_int(&lskflg,fin,swap);
printf("Number Columns = %8d \n",nc);
printf("Number Rows = %8d \n",nr);
printf("Number Sections = %8d \n",ns);
printf("MODE = %4d (only data type mode 2: 32-bit)\n",mode);
printf("NSYMBT = %4d (# bytes symmetry operators)\n",nsymbt);
/* printf(" NCSTART = %8d (index of first column, counting from 0)\n",ncstart);
printf("> NRSTART = %8d (index of first row, counting from 0)\n",nrstart);
printf(" NSSTART = %8d (index of first section, counting from 0)\n",nsstart);
printf(" MX = %8d (# of X intervals in unit cell)\n",mx);
printf(" MY = %8d (# of Y intervals in unit cell)\n",my);
printf(" MZ = %8d (# of Z intervals in unit cell)\n",mz);
printf(" X length = %8.3f (unit cell dimension)\n",xlen);
printf(" Y length = %8.3f (unit cell dimension)\n",ylen);
printf(" Z length = %8.3f (unit cell dimension)\n",zlen);
printf(" Alpha = %8.3f (unit cell angle)\n",a_tmp);
printf(" Beta = %8.3f (unit cell angle)\n",b_tmp);
printf(" Gamma = %8.3f (unit cell angle)\n",g_tmp);
printf(" MAPC = %8d (columns axis: 1=X,2=Y,3=Z)\n",mapc);
printf(" MAPR = %8d (rows axis: 1=X,2=Y,3=Z)\n",mapr);
printf(" MAPS = %8d (sections axis: 1=X,2=Y,3=Z)\n",maps);
printf(" DMIN = %8.3f (minimum density value - ignored)\n",dmin);
printf(" DMAX = %8.3f (maximum density value - ignored)\n",dmax);
printf(" DMEAN = %8.3f (mean density value - ignored)\n",dmean);
printf(" ISPG = %8d (space group number - ignored)\n",ispg);
printf(" NSYMBT = %8d (# bytes storing symmetry operators)\n",nsymbt);
printf(" LSKFLG = %8d (skew matrix flag: 0:none, 1:follows)\n",lskflg);*/
if (header_ok == 0) {
cout << "ERROR reading MRC header: " << filename;
exit(1);
}
if(nr!=param.param_device.NumberPixels || nc!=param.param_device.NumberPixels )
{
cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << nc << ", j " << nr << ")" << "\n";
exit(1);
}
if(mode!=2)
{
cout << "ERROR with MRC mode " << mode << "\n";
cout << "Currently mode 2 is the only one allowed" << "\n";
exit(1);
} else
{
rewind (fin);
for (count=0; count<256; ++count) if (read_float_empty(fin)==0) {
cout << "ERROR Converting Data: " << filename;
exit(1);
}
for (count=0; count<(unsigned long)nsymbt; ++count) if (read_char_float(&currfloat,fin)==0) {
cout << "ERROR Converting Data: " << filename;
exit(1);
}
for ( int nmap = 0 ; nmap < ns ; nmap ++ )
{
st=0.0;
st2=0.0;
for ( int j = 0 ; j < nr ; j ++ )
for ( int i = 0 ; i < nc ; i ++ )
{
if (read_float(&currfloat,fin,swap)==0) {
cout << "ERROR Converting Data: " << filename;
exit(1);
} else {
Ref[nmap+ntotRefMap].points[i][j] = currfloat;
st += currfloat;
st2 += currfloat*currfloat;
}
}
//Normaling maps to zero mean and unit standard deviation
st /= float(nr*nc);
st2 = sqrt(st2/float(nr*nc)-st*st);
for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
Ref[nmap+ntotRefMap].points[i][j] = Ref[nmap+ntotRefMap].points[i][j]/st2 - st/st2;
// if(nmap+ntotRefMap==300)cout << i << " " << j << " " << nmap+ntotRefMap << " " << Ref[nmap+ntotRefMap].points[i][j] << "\n";
}
}
ntotRefMap += ns ;
// cout << ntotRefMap << "\n";
}
fclose (fin);
return(0);
}
int bioem_RefMap::read_float(float *currfloat, FILE *fin, int swap) {
unsigned char *cptr, tmp;
if (fread(currfloat,4,1,fin)!=1) return 0;
if (swap == 1) {
cptr = (unsigned char *)currfloat;
tmp = cptr[0];
cptr[0]=cptr[3];
cptr[3]=tmp;
tmp = cptr[1];
cptr[1]=cptr[2];
cptr[2]=tmp;
}
return 1;
}
int bioem_RefMap::read_int(int *currlong, FILE *fin, int swap) {
unsigned char *cptr, tmp;
if (fread(currlong,4,1,fin)!=1) return 0;
if (swap == 1) {
cptr = (unsigned char *)currlong;
tmp = cptr[0];
cptr[0]=cptr[3];
cptr[3]=tmp;
tmp = cptr[1];
cptr[1]=cptr[2];
cptr[2]=tmp;
}
return 1;
}
int bioem_RefMap::read_float_empty (FILE *fin) {
float currfloat;
if (fread(&currfloat,4,1,fin)!=1) return 0;
return 1;
}
int bioem_RefMap::read_char_float (float *currfloat, FILE *fin) {
char currchar;
if (fread(&currchar,1,1,fin)!=1) return 0;
*currfloat=(float)currchar;
return 1;
}
int bioem_RefMap::test_mrc (const char *vol_file, int swap) {
FILE *fin;
int nc, nr, ns, mx, my, mz;
int mode, ncstart, nrstart, nsstart;
float xlen, ylen, zlen;
int i, header_ok = 1, n_range_viols = 0;
int mapc, mapr, maps;
float alpha, beta, gamma;
float dmin, dmax, dmean, dummy, xorigin, yorigin, zorigin;
fin = fopen(vol_file, "rb");
if( fin == NULL ) {
cout << "ERROR opening MRC: " << vol_file;
exit(1);
}
//* read header info
header_ok *= read_int(&nc,fin,swap);
header_ok *= read_int(&nr,fin,swap);
header_ok *= read_int(&ns,fin,swap);
header_ok *= read_int(&mode,fin,swap);
header_ok *= read_int(&ncstart,fin,swap);
header_ok *= read_int(&nrstart,fin,swap);
header_ok *= read_int(&nsstart,fin,swap);
header_ok *= read_int(&mx,fin,swap);
header_ok *= read_int(&my,fin,swap);
header_ok *= read_int(&mz,fin,swap);
header_ok *= read_float(&xlen,fin,swap);
header_ok *= read_float(&ylen,fin,swap);
header_ok *= read_float(&zlen,fin,swap);
header_ok *= read_float(&alpha,fin,swap);
header_ok *= read_float(&beta,fin,swap);
header_ok *= read_float(&gamma,fin,swap);
header_ok *= read_int(&mapc,fin,swap);
header_ok *= read_int(&mapr,fin,swap);
header_ok *= read_int(&maps,fin,swap);
header_ok *= read_float(&dmin,fin,swap);
header_ok *= read_float(&dmax,fin,swap);
header_ok *= read_float(&dmean,fin,swap);
for (i=23; i<50; ++i) header_ok *= read_float(&dummy,fin,swap);
header_ok *= read_float(&xorigin,fin,swap);
header_ok *= read_float(&yorigin,fin,swap);
header_ok *= read_float(&zorigin,fin,swap);
fclose (fin);
if (header_ok == 0) {
cout << "ERROR reading MRC header: " << vol_file;
exit(1);
}
n_range_viols += (nc>5000); n_range_viols += (nc<0);
n_range_viols += (nr>5000); n_range_viols += (nr<0);
n_range_viols += (ns>5000); n_range_viols += (ns<0);
n_range_viols += (ncstart>5000); n_range_viols += (ncstart<-5000);
n_range_viols += (nrstart>5000); n_range_viols += (nrstart<-5000);
n_range_viols += (nsstart>5000); n_range_viols += (nsstart<-5000);
n_range_viols += (mx>5000); n_range_viols += (mx<0);
n_range_viols += (my>5000); n_range_viols += (my<0);
n_range_viols += (mz>5000); n_range_viols += (mz<0);
n_range_viols += (alpha>360.0f); n_range_viols += (alpha<-360.0f);
n_range_viols += (beta>360.0f); n_range_viols += (beta<-360.0f);
n_range_viols += (gamma>360.0f); n_range_viols += (gamma<-360.0f);
return n_range_viols;
}
model.cpp 100644 → 100755
View file @ 4a123b50
......@@ -109,8 +109,7 @@ int bioem_model::readModel()
}
nPointsModel = numres;
cout << "Protein structure read from PDB\nTotal Number of Residues " << nPointsModel;
cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Protein structure read from PDB\n";
}
else //Reading model from FILE FORMAT x,y,z,rad,density
{
......@@ -118,32 +117,35 @@ int bioem_model::readModel()
int numres = 0;
NormDen = 0.0;
FILE *file = fopen ( filemodel , "r" );
if ( file != NULL )
if (file == NULL)
{
while ( fgets ( line, sizeof line, file ) != NULL )
cout << "Error opening file " << filemode, << "\n";
exit(1);
}
while ( fgets ( line, sizeof line, file ) != NULL )
{
if (numres >= BIOEM_MODEL_SIZE)
{
if (numres >= BIOEM_MODEL_SIZE)
{
cout << "BIOEM_MODEL_SIZE too small\n";
exit(1);
}
float tmpval[5];
sscanf(line, "%f %f %f %f %f", &tmpval[0], &tmpval[1], &tmpval[2], &tmpval[3], &tmpval[4]);
PointsModel[numres].pos[0] = (myfloat_t) tmpval[0];
PointsModel[numres].pos[1] = (myfloat_t) tmpval[1];
PointsModel[numres].pos[2] = (myfloat_t) tmpval[2];
radiusPointsModel[numres] = (myfloat_t) tmpval[3];
densityPointsModel[numres] = (myfloat_t) tmpval[4];
exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " << PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " << densityPointsModel[numres] << "\n";
NormDen += densityPointsModel[numres];
numres++;
cout << "BIOEM_MODEL_SIZE too small\n";
exit(1);
}
nPointsModel = numres;
cout << "Protein structure read from Standard File \nTotal Number of Residues " << nPointsModel ;
cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
float tmpval[5];
sscanf(line, "%f %f %f %f %f", &tmpval[0], &tmpval[1], &tmpval[2], &tmpval[3], &tmpval[4]);
PointsModel[numres].pos[0] = (myfloat_t) tmpval[0];
PointsModel[numres].pos[1] = (myfloat_t) tmpval[1];
PointsModel[numres].pos[2] = (myfloat_t) tmpval[2];
radiusPointsModel[numres] = (myfloat_t) tmpval[3];
densityPointsModel[numres] = (myfloat_t) tmpval[4];
exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " << PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " << densityPointsModel[numres] << "\n";
NormDen += densityPointsModel[numres];
numres++;
}
nPointsModel = numres;
cout << "Protein structure read from Standard File\n";
}
cout << "Total Number of Voxels " << nPointsModel ;
cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
exampleReadCoor.close();
//Moving to Model to its center of mass:
......
param.cpp 100644 → 100755
View file @ 4a123b50
......@@ -42,6 +42,23 @@ int bioem_param::readParameters()
// ***************************** Reading Input Parameters ******************************
// **************************************************************************************
// Control for Parameters
bool yesPixSi = false;
bool yesNumPix = false;
bool yesGPal = false;
bool yesGPbe = false;
bool yesGPEnv = false;
bool yesGPamp = false;
bool yesGPpha = false;
bool yesSTEnv = false;
bool yesSTamp = false;
bool yesSTpha = false;
bool yesGSPamp = false ;
bool yesGSPEnv = false ;
bool yesGSPpha = false ;
bool yesMDC = false ;
bool yesGCen = false ;
ifstream input(fileinput);
if (!input.good())
{
......@@ -70,116 +87,162 @@ int bioem_param::readParameters()
{
token = strtok(NULL, " ");
pixelSize = atof(token);
cout << "Pixel Sixe " << pixelSize << "\n";
if (pixelSize < 0 ) { cout << "*** Error: Negative pixelSize "; exit(1);}
cout << "Pixel Sixe " << pixelSize << "\n";
yesPixSi= true;
}
else if (strcmp(token, "NUMBER_PIXELS") == 0)
{
token = strtok(NULL, " ");
param_device.NumberPixels = int(atoi(token));
cout << "Number of Pixels " << param_device.NumberPixels << "\n";
if (param_device.NumberPixels < 0 ) { cout << "*** Error: Negative Number of Pixels "; exit(1);}
cout << "Number of Pixels " << param_device.NumberPixels << "\n";
yesNumPix= true ;
}
else if (strcmp(token, "GRIDPOINTS_ALPHA") == 0)
{
token = strtok(NULL, " ");
angleGridPointsAlpha = int(atoi(token));
cout << "Grid points alpha " << angleGridPointsAlpha << "\n";
if (angleGridPointsAlpha < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ALPHA "; exit(1);}
cout << "Grid points alpha " << angleGridPointsAlpha << "\n";
yesGPal= true;
}
else if (strcmp(token, "GRIDPOINTS_BETA") == 0)
{
token = strtok(NULL, " ");
angleGridPointsBeta = int(atoi(token));
cout << "Grid points beta " << angleGridPointsBeta << "\n";
if (angleGridPointsBeta < 0 ) { cout << "*** Error: Negative GRIDPOINTS_BETA "; exit(1);}
cout << "Grid points beta " << angleGridPointsBeta << "\n";
yesGPbe= true;
}
else if (strcmp(token, "GRIDPOINTS_ENVELOPE") == 0)
{
token = strtok(NULL, " ");
numberGridPointsEnvelop = int(atoi(token));
cout << "Grid points envelope " << numberGridPointsEnvelop << "\n";
if (numberGridPointsDisplaceCenter < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ENVELOPE "; exit(1);}
cout << "Grid points envelope " << numberGridPointsEnvelop << "\n";
yesGPEnv = true;
}
else if (strcmp(token, "START_ENVELOPE") == 0)
{
token = strtok(NULL, " ");
startGridEnvelop = atof(token);
cout << "Start Envelope " << startGridEnvelop << "\n";