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#!/bin/bash
. ../MasterTest.sh
CleanFiles modes.in fluct.dat displ.dat corr.dat modestest.2.crd eigenval.dat rmsip.dat
INPUT='modes.in'
TESTNAME='Modes Analysis'
Requires mathlib
# Test modes fluct and mwcovar matrix generation
TestFluct() {
UNITNAME='Modes analysis, RMS fluctuations'
CheckFor netcdf
if [ $? -eq 0 ] ; then
TOP=../tz2.parm7
cat > modes.in <<EOF
trajin ../tz2.nc
matrix mwcovar name tz2 @CA
diagmatrix tz2 name tz2modes vecs 20
modes fluct name tz2modes out fluct.dat setname Fluct prec 10.3
EOF
RunCpptraj "$UNITNAME"
DoTest fluct.dat.save fluct.dat
fi
}
# Test modes displ and modes file read
TestDispl() {
TOP=../tz2.parm7
# Since the displacement test can be fooled by eigenvector
# sign flips, read in a previously generated set of modes.
cat > modes.in <<EOF
readdata tz2.evecs.dat name tz2modes
analyze modes displ name tz2modes out displ.dat setname Displ prec 10.3
EOF
RunCpptraj "Modes analysis, displacements"
DoTest displ.dat.save displ.dat
}
# Test modes corr and mwcovar matrix generation
TestCorr() {
UNITNAME='Modes analysis, dipole correlation'
CheckFor netcdf
if [ $? -eq 0 ] ; then
TOP=../tz2.parm7
cat > modes.in <<EOF
trajin ../tz2.nc
matrix mwcovar name tz2
analyze matrix tz2 name tz2modes vecs 20
analyze modes corr name tz2modes out corr.dat mask1 :2-13@N mask2 :2-13@H
EOF
RunCpptraj "$UNITNAME"
DoTest corr.dat.save corr.dat
fi
}
# Test modes trajout
TestTrajout() {
TOP="INPpYLYP.FF14SB.parm7"
cat > modes.in <<EOF
readdata evecs.dat name evecs
modes name evecs trajout modestest.2.crd pcmin -33 pcmax 46 tmode 2 trajoutmask !@H=
EOF
RunCpptraj "Modes analysis, pseudo trajectory creation test"
DoTest modestest.2.crd.save modestest.2.crd
}
# Test modes RMSIP and eigenval
TestRMSIP() {
cat > modes.in <<EOF
readdata evecs.dat name evecs
readdata evecs2.dat name evecs2
modes name evecs name2 evecs2 rmsip beg 1 end 5 out rmsip.dat setname RMSIP
modes name evecs eigenval out eigenval.dat setname EV prec 12.6
EOF
RunCpptraj "Modes analysis, RMSIP and eigenvalue fraction test"
DoTest rmsip.dat.save rmsip.dat
DoTest eigenval.dat.save eigenval.dat
}
TestFluct
TestDispl
TestCorr
TestTrajout
TestRMSIP
EndTest
exit 0
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