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/*****************************************************************************
TRAVIS - Trajectory Analyzer and Visualizer
http://www.travis-analyzer.de/
Copyright (c) 2009-2019 Martin Brehm
2012-2019 Martin Thomas
2016-2019 Sascha Gehrke
This file was written by Martin Brehm.
---------------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
// This must always be the first include directive
#include "config.h"
#include "order.h"
#include "order_chain.h"
#include "globalvar.h"
#include "maintools.h"
const char *GetRevisionInfo_order_chain(unsigned int len) {
static char buf[256];
GET_REVISION_INFO( buf, len );
return buf;
}
const char *GetSourceVersion_order_chain() {
static char buf[256];
GET_SOURCE_VERSION( buf );
return buf;
}
bool COrderAnalysis_Chain::Parse(CTimeStep *ts) {
int z;
//CMolecule *m;
//CSingleMolecule *sm;
CxString buf;
UNUSED(ts);
mprintf(WHITE,"\n >>> Analysis %d: Alkyl Chain Order Parameters >>>\n\n",m_iNumber+1);
if (g_oaMolecules.GetSize() == 1) {
mprintf(" Using molecule 1.\n");
m_iMolecule = 0;
} else
m_iMolecule = AskRangeInteger_ND(" Define vectors in which molecule (1-%d)? ",1,g_oaMolecules.GetSize(),g_oaMolecules.GetSize()) - 1;
if (m_pParent->m_oaChains[m_iMolecule].size() == 0) {
eprintf("\n Error: No alkyl chains have been detected in molecule %d.\n",m_iMolecule+1);
abort();
}
//m = (CMolecule*)g_oaMolecules[m_iMolecule];
_ilagain:
m_iaChains.clear();
AskString_ND(" Which chain(s) to use in molecule %d (comma separated, see list above)? ",&buf,m_iMolecule+1);
if (!ParseIntList((const char*)buf,m_iaChains)) {
eprintf("\n Invalid input.\n\n");
goto _ilagain;
}
for (z=0;z<(int)m_iaChains.size();z++) {
if ((m_iaChains[z] < 1) || (m_iaChains[z] > (int)m_pParent->m_oaChains[m_iMolecule].size())) {
eprintf("\n Chain number %d outside of allowed range (%d .. %lu).\n\n",m_iaChains[z],1,m_pParent->m_oaChains[m_iMolecule].size());
goto _ilagain;
}
m_iaChains[z]--;
if (z > 0) {
if (m_pParent->m_oaChains[m_iMolecule][m_iaChains[0]]->m_iaAtoms.size() != m_pParent->m_oaChains[m_iMolecule][m_iaChains[z]]->m_iaAtoms.size()) {
eprintf("\n Chains have different lengths (%d: %lu vs. %d: %lu).\n\n",m_iaChains[0]+1,m_pParent->m_oaChains[m_iMolecule][m_iaChains[0]]->m_iaAtoms.size(),m_iaChains[z]+1,m_pParent->m_oaChains[m_iMolecule][m_iaChains[z]]->m_iaAtoms.size());
goto _ilagain;
}
} else {
if (m_pParent->m_oaChains[m_iMolecule][m_iaChains[0]]->m_iaAtoms.size() < 4) {
eprintf("\n Chains need to have at least length 4 (found: %lu).\n\n",m_pParent->m_oaChains[m_iMolecule][m_iaChains[0]]->m_iaAtoms.size());
goto _ilagain;
}
}
}
mprintf("\n");
m_iDihedrals = (int)m_pParent->m_oaChains[m_iMolecule][m_iaChains[0]]->m_iaAtoms.size()-3;
mprintf(" Using %lu chains of length %lu, therefore %d dihedrals.\n\n",m_iaChains.size(),m_pParent->m_oaChains[m_iMolecule][m_iaChains[0]]->m_iaAtoms.size(),m_iDihedrals);
m_bSaveHistograms = AskYesNo(" Save histogram for each group of dihedrals (y/n)? [yes] ",true);
m_faGauche.resize(m_iDihedrals);
m_faTotal.resize(m_iDihedrals);
m_faEcliptic1.resize(m_iDihedrals);
m_faEcliptic2.resize(m_iDihedrals);
for (z=0;z<m_iDihedrals;z++) {
m_faGauche[z] = 0;
m_faTotal[z] = 0;
m_faEcliptic1[z] = 0;
m_faEcliptic2[z] = 0;
}
m_fGaucheCount = 0;
m_fGaucheSqSum = 0;
m_fCountTotal = 0;
m_pGaucheCountHistogram = new CDF();
m_pGaucheCountHistogram->m_fMinVal = 0;
m_pGaucheCountHistogram->m_fMaxVal = (double)m_iDihedrals+1.0;
m_pGaucheCountHistogram->m_iResolution = (int)m_iDihedrals+1;
m_pGaucheCountHistogram->Create();
m_pGaucheCountHistogram->SetLabelX("Number of Gauche Dihedrals in Chain");
m_pGaucheCountHistogram->SetLabelY("Occurrence");
m_pGaucheCountHistogram->m_bLeft = true;
if (m_bSaveHistograms) {
m_oaHistograms.resize(m_iDihedrals);
for (z=0;z<m_iDihedrals;z++) {
m_oaHistograms[z] = new CDF();
m_oaHistograms[z]->m_fMinVal = 0;
m_oaHistograms[z]->m_fMaxVal = 180.0;
m_oaHistograms[z]->m_iResolution = 100;
m_oaHistograms[z]->Create();
m_oaHistograms[z]->SetLabelX("Dihedral Angle");
m_oaHistograms[z]->SetLabelY("Occurrence");
}
}
mprintf(WHITE,"\n <<< Analysis %d: Alkyl Chain Order Parameters <<<\n\n",m_iNumber+1);
return true;
}
void COrderAnalysis_Chain::ProcessStep(CTimeStep *ts) {
int z, z2, z3, i;
CMolecule *m;
CSingleMolecule *sm;
COrderChain *oc;
double tf;
m = (CMolecule*)g_oaMolecules[m_iMolecule];
for (z=0;z<m->m_laSingleMolIndex.GetSize();z++) {
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z]];
for (z2=0;z2<(int)m_iaChains.size();z2++) {
oc = m_pParent->m_oaChains[m_iMolecule][m_iaChains[z2]];
i = 0;
for (z3=0;z3<m_iDihedrals;z3++) {
tf = Dihedral(
FoldVector(ts->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[oc->m_iCarbonIndex])->GetAt(oc->m_iaAtoms[z3])]
- ts->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[oc->m_iCarbonIndex])->GetAt(oc->m_iaAtoms[z3+1])]),
FoldVector(ts->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[oc->m_iCarbonIndex])->GetAt(oc->m_iaAtoms[z3+3])]
- ts->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[oc->m_iCarbonIndex])->GetAt(oc->m_iaAtoms[z3+2])]),
FoldVector(ts->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[oc->m_iCarbonIndex])->GetAt(oc->m_iaAtoms[z3+1])]
- ts->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[oc->m_iCarbonIndex])->GetAt(oc->m_iaAtoms[z3+2])]),
true
);
if (m_bSaveHistograms)
m_oaHistograms[z3]->AddToBin(tf);
if (tf < 120.0) {
i++;
m_faGauche[z3]++;
}
if (tf < 20.0)
m_faEcliptic1[z3]++;
if ((tf > 100.0) && (tf < 140.0))
m_faEcliptic2[z3]++;
m_faTotal[z3]++;
}
m_fGaucheCount += (double)i/m_iDihedrals;
m_fGaucheSqSum += (double)i*i/m_iDihedrals/m_iDihedrals;
m_fCountTotal++;
m_pGaucheCountHistogram->AddToBin((double)i);
}
}
}
void COrderAnalysis_Chain::Finish() {
int z;
double mean, sd;
CxString buf;
FILE *a;
mprintf(WHITE,"\n *** Chain Order Parameter Analysis %d ***\n\n",m_iNumber+1);
for (z=0;z<m_iDihedrals;z++) {
mprintf(" Dihedral %2d: %5.2f%c Gauche, %5.2f%c Ecliptic 1, %5.2f%c Ecliptic 2, %.0f hits.\n",z+1,m_faGauche[z]/m_faTotal[z]*100.0,'%',m_faEcliptic1[z]/m_faTotal[z]*100.0,'%',m_faEcliptic2[z]/m_faTotal[z]*100.0,'%',m_faTotal[z]);
if (m_bSaveHistograms) {
buf.sprintf("order_chain%d_histogram_%d.csv",m_iNumber+1,z+1);
mprintf(" Saving histogram to %s ...\n",(const char*)buf);
m_oaHistograms[z]->NormBinSum(100.0);
m_oaHistograms[z]->Write((const char*)buf,"","",false);
}
}
mprintf("\n");
buf.sprintf("order_chain%d_results.csv",m_iNumber+1);
mprintf(" Saving results to %s ...\n",(const char*)buf);
a = OpenFileWrite((const char*)buf,true);
mfprintf(a,"# Dihedral; Gauche percentage; Anti percentage; Ecliptic 1 percentage; Ecliptic 2 percentage\n");
for (z=0;z<m_iDihedrals;z++)
mfprintf(a,"%d; %.6f; %.6f; %.6f; %.6f\n",
z+1,
m_faGauche[z]/m_faTotal[z]*100.0,
(1.0-m_faGauche[z]/m_faTotal[z])*100.0,
m_faEcliptic1[z]/m_faTotal[z]*100.0,
m_faEcliptic2[z]/m_faTotal[z]*100.0
);
fclose(a);
mprintf("\n");
mean = m_fGaucheCount/m_fCountTotal;
sd = sqrt(m_fGaucheSqSum/m_fCountTotal - mean*mean);
mprintf(" Average Gauche count per chain is %.3f%c +/- %.3f%c.\n",mean*100.0,'%',100.0*sd,'%');
mprintf(" (Uncertainty is the standard deviation)\n\n");
buf.sprintf("order_chain%d_gauchecount.csv",m_iNumber+1);
mprintf(" Saving Gauche count histogram to %s ...\n",(const char*)buf);
m_pGaucheCountHistogram->NormBinSum(100.0);
m_pGaucheCountHistogram->Write((const char*)buf,"","",false);
mprintf("\n");
}
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