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#!/bin/bash
# Test of IRED
. ../MasterTest.sh
CleanFiles orderparam ired.vec noe v0.cjt v0.cmt ired.in v0 plateau.norm.dat cjt?.dat \
matrix_ds2.dat
TESTNAME='IRED vector/matrix test'
Requires mathlib
TOP="1IEE_A_prot.prmtop"
INPUT="ired.in"
cat > $INPUT <<EOF
trajin 1IEE_A_test.mdcrd
for atoms Natom inmask :2-129@N&!:PRO atoms Hatom inmask :2-129@H v=1;v++
vector v\$v \$Natom ired \$Hatom
done
matrix ired name matired order 2
diagmatrix matired out ired.vec name ired.vec vecs \$v
ired order 2 modes ired.vec relax freq 500.0 NHdist 1.02 \
tstep 1.0 tcorr 10000.0 norm name MyIred \
out v0 noefile noe ds2matrix matrix_ds2.dat
datafile v0.cmt noheader
datafile v0.cjt noheader
create plateau.norm.dat MyIred[Plateau] noxcol prec 12.8 noheader
create orderparam MyIred[S2] prec 10.5
run
writedata cjt1.dat MyIred[Cj(t)]:0
EOF
RunCpptraj "$TESTNAME"
#DoTest ired.vec.save ired.vec
#DoTest v0.cmt.new.norm.save v0.cmt
#DoTest plateau.norm.dat.save plateau.norm.dat
#DoTest v0.cjt.new.save v0.cjt
#DoTest orderparam.save orderparam
#DoTest matrix_ds2.dat.save matrix_ds2.dat
#DoTest noe.save noe
#DoTest v0.cjt.save v0.cjt
#DoTest v0.cmt.save v0.cmt
EndTest
exit 0
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