#P HF/6-31G(d) opt=Z-Matrix
HCN to CNH isomerization pathway, HF/6-31G(d)
0 1
N1
C2 1 r2
H3 2 r3 1 a3
r2=1.2
r3=1.1
a3=170.0 S 16 -10.0
Wednesday, November 27, 2013
Gaussian transition state scan input file
Monday, November 25, 2013
gnuplot: some scripts and tips
script:
COLVAR gnuplot script.
set xrange [0:1]
set yrange [0:10]
plot "COLVAR" u ($1/120*20*0.0242*6/1000):2 t "CV C1" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):3 t " C2" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):4 t " F1" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):5 t "an F2" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):6 t " H1" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):7 t " H2" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):8 t " H3" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):9 t " H4" w l, \
"COLVAR" u ($1/120*20*0.0242*6/1000):10 t " H5" w l
set output "colvar.jpg"
set terminal jpeg
replot
-----------------------------------------------------------------------------------------
KS energy script file
set xrange [0:29.1]
set yrange [0:160]
plot "ENERGIES" u ($1*0.0242*6/1000):($4+55.9)*2625.50/4.18 notitle w l
set output "1000k-ch3oh-o2-no4-Eksvstime-ps-v2.jpg"
set terminal jpeg
replot
---------------------------------------------------------------------------------------
multiple script file
set output "h-so2-Eksvstime-sprint-ps.jpg"
set terminal jpeg
set multiplot layout 3,1
#set tmargin 0.2
#set bmargin 0.8
set lmargin 5
#set rmargin 5
set xrange [0:4.35]
set yrange [0:320]
set ytic 0,50,300
set format x " "
plot "ENERGIES" u ($1-10500)*6*0.0242/1000:(($4+42.54)*2625.50) notitle w l
set xrange [0:4.35]
set yrange [0:80]
set ytic 0,20,60
set format x " "
plot "ENERGIES" u ($1-10500)*6*0.0242/1000:($2*2625.50) notitle w l
set xrange [0:4.35]
set yrange [0:3.0]
set ytic 0,1.0,2.5
set key center bottom
set key spacing .6
set key font ",6"
set format x " %g "
plot "COLVAR" u ($1/120*20-10500)*6*0.0242/1000:2 t "SPRINT S1" w l, \
"COLVAR" u ($1/120*20-10500)*6*0.0242/1000:3 t " O1" w l, \
"COLVAR" u ($1/120*20-10500)*6*0.0242/1000:4 t " O2" w l, \
"COLVAR" u ($1/120*20-10500)*6*0.0242/1000:5 t " H1" w l
unset multiplot
set output
Friday, November 22, 2013
metadynamic and well-tempered metadynamics
well tempered mtd
------------------------------------------------------------------
# CPMD units are a.u.: energy = hartree, distance = bohr, time = 0.024 fs
HILLS HEIGHT 0.00009 W_STRIDE 50
WELLTEMPERED SIMTEMP 300 BIASFACTOR 10
PRINT W_STRIDE 20
g1->
1 2 3 4 5 6 8 9 10 11 12
g1<- p="">
POSITION LIST SIGMA 0.35 DIR Z
ENDMETA
------------------------------------------------------------------
# CPMD units are a.u.: energy = hartree, distance = bohr, time = 0.024 fs
HILLS HEIGHT 0.00009 W_STRIDE 50
WELLTEMPERED SIMTEMP 300 BIASFACTOR 10
PRINT W_STRIDE 20
g1->
1 2 3 4 5 6 8 9 10 11 12
g1<- p="">
POSITION LIST
ENDMETA
MTD
-------------------------------------------------------------------
# CPMD units are a.u.: energy = hartree, distance = bohr, time = 0.024 fs
HILLS RESTART HEIGHT 0.009 W_STRIDE 300
PRINT W_STRIDE 20
all->
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
all<- div="">
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 1 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 2 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 3 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 4 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 5 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 6 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 7 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 8 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 9 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 10 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 11 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 12 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 13 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 14 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 15 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 16 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 17 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 18 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 19 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 20 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 21 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 22 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 23 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 24 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 25 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 26 SIGMA 1.5
SPRINT LIST NN 6 MM 12 R_0 10 5.0 5.0 5.0 4.2 5.0 5.0 4.2 5.0 4.2 4.2 INDEX 27 SIGMA 1.5
RGYR LIST SIGMA 1.5
NOHILLS CV 28
UWALL CV 28 LIMIT 8.00 KAPPA 0.5 EXP 2
ENDMETA
Thursday, November 21, 2013
Gaussian some input files for transition states
pbs file
#!/bin/bash
#PBS -N test
#PBS -l nodes=1:ppn=8
#PBS -l walltime=8:00:00
#PBS -j oe
### this will send and email when your job's status changes
### Specify the app to run here ###
### ###
cd $PBS_O_WORKDIR
export g09root="/codes/G09"
export GAUSS_SCRDIR=$PBS_O_WORKDIR
#GAUSS_SCRDIR="/GAUSS_SCRATCH"
#export g09root GAUSS_SCRDIR
. $g09root/g09/bsd/g09.profile
## AND NOW WE DO A CALCUATION
## g09 test.com
g09 nofre.com
## g09 opt.com
### include any post processing here ###
### ###
#
exit 0
-----------------------------------------------------------------------------------------------------
qst2
%chk=ts-ch3oh-o2.chk
%nprocshared=8
%mem=16gb
# HF/6-31G* opt(qst2)
reactants
0,3
C -3.177481 1.256011 -0.187008
O -2.284301 2.342144 -0.515577
O 0.492876 -1.214734 -0.800401
O 0.426581 -1.291085 0.456829
H -4.238756 1.523717 -0.259563
H -2.955856 1.011776 0.884952
H -2.897823 0.467761 -0.819904
H -2.002079 2.824345 0.282715
products
0,3
C -1.645926 -0.498130 -1.077528
O -0.653966 -0.919073 -0.210084
O -0.966639 2.622203 -0.355541
O -1.547804 2.285127 0.638756
H -1.389444 1.733866 -1.118653
H -2.380255 0.183607 -0.458397
H -1.835573 -1.384190 -1.610873
H -0.680901 -0.013826 0.290209
#!/bin/bash
#PBS -N test
#PBS -l nodes=1:ppn=8
#PBS -l walltime=8:00:00
#PBS -j oe
### this will send and email when your job's status changes
### Specify the app to run here ###
### ###
cd $PBS_O_WORKDIR
export g09root="/codes/G09"
export GAUSS_SCRDIR=$PBS_O_WORKDIR
#GAUSS_SCRDIR="/GAUSS_SCRATCH"
#export g09root GAUSS_SCRDIR
. $g09root/g09/bsd/g09.profile
## AND NOW WE DO A CALCUATION
## g09 test.com
g09 nofre.com
## g09 opt.com
### include any post processing here ###
### ###
#
exit 0
qst2
%chk=ts-ch3oh-o2.chk
%nprocshared=8
%mem=16gb
# HF/6-31G* opt(qst2)
reactants
0,3
C -3.177481 1.256011 -0.187008
O -2.284301 2.342144 -0.515577
O 0.492876 -1.214734 -0.800401
O 0.426581 -1.291085 0.456829
H -4.238756 1.523717 -0.259563
H -2.955856 1.011776 0.884952
H -2.897823 0.467761 -0.819904
H -2.002079 2.824345 0.282715
products
0,3
C -1.645926 -0.498130 -1.077528
O -0.653966 -0.919073 -0.210084
O -0.966639 2.622203 -0.355541
O -1.547804 2.285127 0.638756
H -1.389444 1.733866 -1.118653
H -2.380255 0.183607 -0.458397
H -1.835573 -1.384190 -1.610873
H -0.680901 -0.013826 0.290209
----------------------------------------------------------------------------------------------------------
qst3
%chk=ts-ch3oh-o2.chk
%nprocshared=8
%mem=16gb
# HF/6-31G* opt(qst3)
reactants
0,3
C -1.831936 -0.455294 -1.000156
O -0.493883 -0.890046 -0.235749
O -0.766284 1.611589 -0.147007
O -1.805811 1.258415 0.542778
H -1.655954 0.534975 -1.543149
H -2.343630 -0.276478 -0.109751
H -2.120258 -1.175328 -1.691490
H -0.381442 -0.063029 0.144704
products
0,3
C -1.900815 -0.845392 -0.927500
O -0.665315 -0.785582 -0.219485
O -1.001482 1.767697 -0.378953
O -1.532152 1.101734 0.691260
H -0.132511 1.357497 -0.774537
H -2.655260 0.101360 -0.672792
H -1.549617 -1.018987 -1.970438
H -0.674073 0.069990 0.341985
transition state
0,3
C -1.645926 -0.498130 -1.077528
O -0.653966 -0.919073 -0.210084
O -0.966639 1.622203 -0.355541
O -1.612905 1.247369 0.750135
H -1.389444 0.733866 -1.118653
H -2.380255 0.183607 -0.458397
H -1.835573 -1.384190 -1.610873
H -0.680901 -0.013826 0.290209
------------------------------------------------------------------------------------------------
direct ts opt file
%chk=ts-ch3oh-o2.chk
%nprocshared=8
%mem=16gb
# BLYP/6-311+G** opt(calcall,ts,noeigen,maxcycle=1000, Cartesian) freq scf=maxcycle=1000 nosymm
this is a test for ts
0,3
C -1.645926 -0.498130 -1.077528
O -0.653966 -0.919073 -0.210084
O -0.966639 1.622203 -0.355541
O -1.547804 1.285127 0.638756
H -1.389444 0.733866 -1.118653
H -2.380255 0.183607 -0.458397
H -1.835573 -1.384190 -1.610873
H -0.680901 -0.013826 0.290209
Wednesday, November 20, 2013
perl and bash scripts
killjobs.sh
for ((i=1082042;i<1082096 br="" i="">do
qdel $i.login1
done
echo "all jobs done!"
---------------------------------------------------------------------------
makefile.sh
i=0
for ((i=0;i<20 br="" i="">do
mkdir ch3oh-o2$i
cat inputpart1 o2part$i inputpart2 >> input-o2-$i
cat inputpart1-pro o2part$i inputpart2 >> input-o2-$i-pro
mv input-o2-$i ch3oh-o2$i/input
mv input-o2-$i-pro ch3oh-o2$i/input-pro
cp cpmdrun.pbs plumed.dat plumed-pro.dat ch3oh-o2$i
done
#for ((i=0;i<10 br="" i="">#do
#cd ch3oh-oxy$i
#qsub cpmdrun.pbs
#cd ..
#done
rm o2part*
echo "all jobs done!"
--------------------------------------------------------------------------------------------
read-o2.pl
#! /usr/bin/perl -w
my @line=0;
my $i=0;
open FILE1, "20noatomo2methanol.xyz" or die $!;
@line=;
for ($i=0;$i<20 br="" i="">open FILE2, "> o2part$i";
print FILE2 $line[2*$i];
print FILE2 $line[2*$i+1];
close FILE2;
}
close FILE1;
------------------------------------------------------------------------------------------------------
use-findall.sh
i=0
mkdir all-fourfiles
for ((i=0;i<4 br="" i="">do
./find-1214161820.pl ch3oh-o2$i/production/TRAJEC.xyz
mv requiredTimestepsCordinates.xyz all-fourfiles/coordinate$i.xyz
done
echo "all jobs done!"
------------------------------------------------------------------------------------------------------
sum_wham.sh
#!/bin/bash
metafile=wham_metafile
fesout=fes.out
rm -rf $metafile $fesout
points=1000 #there are 500 points/COLVAR, we'll not count the 1st 50 for equilibration.
## important note! Umbrella sampling uses a potential like
## V = 1/2 kappa (CV - CV(0))^2 but UWALL/LWALL don't have the 1/2 in there. So if you are using
## UWALL/LWALL to do your umbrella sampling, then you need to multiply your K value by 2!
for file in shortp? longp? longp??; do
tail -n $points $file/COLVAR | awk '{print $1,$2}' > $file/whamcv;
## get kappa value - multiply by 2
kappa=`grep UMBRELLA $file/plumed.dat | head -n 1 | awk '{print $5}'`
## get umbrella center
PV=`grep UMBRELLA $file/plumed.dat | head -n 1 | awk '{print $7}'`
echo $file/whamcv $PV $kappa >> wham_metafile
done;
first=`sort -n -k2 wham_metafile | awk '{print $2}' | head -n 1 `
last=`sort -n -k2 wham_metafile | awk '{print $2}' | tail -n 1 `
num=`wc -l wham_metafile | awk '{print $1}'`
tol=$1
wham $first $last $num 0.0001 300 0 $metafile $fesout$tol
--------------------------------------------------------------------------------------------------
read-operate.pl ! to generate the z direction small changes
#! /usr/bin/perl -w
use warnings;
use strict;
my $i=0;
my @total;
my @data1;
my @data2;
my @data3;
my @data4;
my @data5;
my @data6;
open FILE, 'cgeo.xyz' or die "without such a file, $!";
while () {
$total[$i]=$_;
$i++;
}
#print $total[0];
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
#my $test=pop @data1;
#print scalar $data1[1];
#print scalar @data1;
for($i=1;$i<61 file="" i="">
$data1[3]=$data1[3]+0.0529;
$data2[3]=$data2[3]+0.0529;
$data3[3]=$data3[3]+0.0529;
$data4[3]=$data4[3]+0.0529;
$data5[3]=$data5[3]+0.0529;
$data6[3]=$data6[3]+0.0529;
open DATA, ">clongp$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
for($i=1;$i<11 file="" i="">
$data1[3]=$data1[3]-0.0529;
$data2[3]=$data2[3]-0.0529;
$data3[3]=$data3[3]-0.0529;
$data4[3]=$data4[3]-0.0529;
$data5[3]=$data5[3]-0.0529;
$data6[3]=$data6[3]-0.0529;
open DATA, ">clongp-$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
#print @total;
#print "@data1";
$i=0;
open FILEH, 'hgeo.xyz' or die "without such a file, $!";
while () {
$total[$i]=$_;
$i++;
}
#print $total[0];
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
#my $test=pop @data1;
#print scalar $data1[1];
#print scalar @data1;
for($i=1;$i<61 br="" i="">$data1[3]=$data1[3]+0.0529;
$data2[3]=$data2[3]+0.0529;
$data3[3]=$data3[3]+0.0529;
$data4[3]=$data4[3]+0.0529;
$data5[3]=$data5[3]+0.0529;
$data6[3]=$data6[3]+0.0529;
open DATA, ">hlongp$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
for($i=1;$i<11 br="" i="">$data1[3]=$data1[3]-0.0529;
$data2[3]=$data2[3]-0.0529;
$data3[3]=$data3[3]-0.0529;
$data4[3]=$data4[3]-0.0529;
$data5[3]=$data5[3]-0.0529;
$data6[3]=$data6[3]-0.0529;
open DATA, ">hlongp-$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
for ((i=1082042;i<1082096 br="" i="">do
qdel $i.login1
done
echo "all jobs done!"
---------------------------------------------------------------------------
makefile.sh
i=0
for ((i=0;i<20 br="" i="">do
mkdir ch3oh-o2$i
cat inputpart1 o2part$i inputpart2 >> input-o2-$i
cat inputpart1-pro o2part$i inputpart2 >> input-o2-$i-pro
mv input-o2-$i ch3oh-o2$i/input
mv input-o2-$i-pro ch3oh-o2$i/input-pro
cp cpmdrun.pbs plumed.dat plumed-pro.dat ch3oh-o2$i
done
#for ((i=0;i<10 br="" i="">#do
#cd ch3oh-oxy$i
#qsub cpmdrun.pbs
#cd ..
#done
rm o2part*
echo "all jobs done!"
--------------------------------------------------------------------------------------------
read-o2.pl
#! /usr/bin/perl -w
my @line=0;
my $i=0;
open FILE1, "20noatomo2methanol.xyz" or die $!;
@line=
for ($i=0;$i<20 br="" i="">open FILE2, "> o2part$i";
print FILE2 $line[2*$i];
print FILE2 $line[2*$i+1];
close FILE2;
}
close FILE1;
------------------------------------------------------------------------------------------------------
use-findall.sh
i=0
mkdir all-fourfiles
for ((i=0;i<4 br="" i="">do
./find-1214161820.pl ch3oh-o2$i/production/TRAJEC.xyz
mv requiredTimestepsCordinates.xyz all-fourfiles/coordinate$i.xyz
done
echo "all jobs done!"
------------------------------------------------------------------------------------------------------
sum_wham.sh
#!/bin/bash
metafile=wham_metafile
fesout=fes.out
rm -rf $metafile $fesout
points=1000 #there are 500 points/COLVAR, we'll not count the 1st 50 for equilibration.
## important note! Umbrella sampling uses a potential like
## V = 1/2 kappa (CV - CV(0))^2 but UWALL/LWALL don't have the 1/2 in there. So if you are using
## UWALL/LWALL to do your umbrella sampling, then you need to multiply your K value by 2!
for file in shortp? longp? longp??; do
tail -n $points $file/COLVAR | awk '{print $1,$2}' > $file/whamcv;
## get kappa value - multiply by 2
kappa=`grep UMBRELLA $file/plumed.dat | head -n 1 | awk '{print $5}'`
## get umbrella center
PV=`grep UMBRELLA $file/plumed.dat | head -n 1 | awk '{print $7}'`
echo $file/whamcv $PV $kappa >> wham_metafile
done;
first=`sort -n -k2 wham_metafile | awk '{print $2}' | head -n 1 `
last=`sort -n -k2 wham_metafile | awk '{print $2}' | tail -n 1 `
num=`wc -l wham_metafile | awk '{print $1}'`
tol=$1
wham $first $last $num 0.0001 300 0 $metafile $fesout$tol
--------------------------------------------------------------------------------------------------
read-operate.pl ! to generate the z direction small changes
#! /usr/bin/perl -w
use warnings;
use strict;
my $i=0;
my @total;
my @data1;
my @data2;
my @data3;
my @data4;
my @data5;
my @data6;
open FILE, 'cgeo.xyz' or die "without such a file, $!";
while (
$total[$i]=$_;
$i++;
}
#print $total[0];
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
#my $test=pop @data1;
#print scalar $data1[1];
#print scalar @data1;
for($i=1;$i<61 file="" i="">
$data2[3]=$data2[3]+0.0529;
$data3[3]=$data3[3]+0.0529;
$data4[3]=$data4[3]+0.0529;
$data5[3]=$data5[3]+0.0529;
$data6[3]=$data6[3]+0.0529;
open DATA, ">clongp$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
for($i=1;$i<11 file="" i="">
$data2[3]=$data2[3]-0.0529;
$data3[3]=$data3[3]-0.0529;
$data4[3]=$data4[3]-0.0529;
$data5[3]=$data5[3]-0.0529;
$data6[3]=$data6[3]-0.0529;
open DATA, ">clongp-$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
#print @total;
#print "@data1";
$i=0;
open FILEH, 'hgeo.xyz' or die "without such a file, $!";
while (
$total[$i]=$_;
$i++;
}
#print $total[0];
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
#my $test=pop @data1;
#print scalar $data1[1];
#print scalar @data1;
for($i=1;$i<61 br="" i="">$data1[3]=$data1[3]+0.0529;
$data2[3]=$data2[3]+0.0529;
$data3[3]=$data3[3]+0.0529;
$data4[3]=$data4[3]+0.0529;
$data5[3]=$data5[3]+0.0529;
$data6[3]=$data6[3]+0.0529;
open DATA, ">hlongp$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
@data1=split /\s+ /, $total[0];
@data2=split /\s+ /, $total[1];
@data3=split /\s+ /, $total[2];
@data4=split /\s+ /, $total[3];
@data5=split /\s+ /, $total[4];
@data6=split /\s+ /, $total[5];
for($i=1;$i<11 br="" i="">$data1[3]=$data1[3]-0.0529;
$data2[3]=$data2[3]-0.0529;
$data3[3]=$data3[3]-0.0529;
$data4[3]=$data4[3]-0.0529;
$data5[3]=$data5[3]-0.0529;
$data6[3]=$data6[3]-0.0529;
open DATA, ">hlongp-$i";
print DATA "@data1\n";
print DATA "@data2\n";
print DATA "@data3\n";
print DATA "@data4\n";
print DATA "@data5\n";
print DATA "@data6\n";
close (DATA);
}
perl and bash scripts ---II
read-water.pl
#! /usr/bin/perl -w
my @line=0;
my $i=0;
open FILE1, "10waterch3och3noatom.xyz" or die $!;
@line=;
for ($i=0;$i<10 br="" i="">open FILE2, "> water-opart$i";
open FILE3, "> water-hpart$i";
print FILE2 $line[3*$i];
print FILE3 $line[3*$i+1];
print FILE3 $line[3*$i+2];
close FILE2;
close FILE3;
}
close FILE1;
------------------------------------------------------------------------------------------------------
std.pl
#! /usr/bin/perl -w -l
my @eksenergy=0;
my $tempnumber=0;
my $nobias_average_energy=0;
my $product_average_energy=0;
my $temptotal=0;
my $count=0;
my $energy_std=0;
my $selected_range_start=0;
my $selected_range_end=35000;
open ENERGYFILE, 'eks.dat' or die 'can not find the file!';
while (){
$eksenergy[$tempnumber]=$_;
$tempnumber++;
}
close ENERGYFILE;
print 'total numbers are ', $tempnumber;
for ($count=$selected_range_start;$count<$selected_range_end; $count++){
$temptotal=$eksenergy[$count]+$temptotal;
}
$nobias_average_energy=$temptotal/($selected_range_end-$selected_range_start);
$temptotal=0;
for ($count=$selected_range_start;$count<$selected_range_end;$count++){
$temptotal=($eksenergy[$count]-$nobias_average_energy)**2+$temptotal
}
$energy_std=($temptotal/($selected_range_end-$selected_range_start))**(1/2);
print 'the STD is ', $energy_std*627.509;
print 'the average is ', $nobias_average_energy*627.509;
-----------------------------------------------------------------------------------------------------------
decide-h3.pl
#! /usr/bin/perl -w
my @line=0;
my $i=0;
open FILE1, "COLVAR" or die $!;
@line=;
for ($i=0;$i<500 br="" i="">open FILE2, "> hpart$i";
print FILE2 $line[$i];
close FILE2;
}
close FILE1;
-----------------------------------------------------------------------------------------------------------
find-1214161820.pl
#! /usr/bin/perl -w
my @fileContent=0; # array to store contents of a file
my @tempStore=0; # temporary array to store data
my @requiredCoordinates=qw(120001 140001 160001 180001 200001); # get the required time-step coordinates in a TRAJECTORY file.
my $moleculeNumberOfAtoms=8; # the number of one system: methanol and oxygen
my $numberOfSeparation=2; # the separation lines between two coordinate file
my $tempNumber=0; # the temporary number used in program
my $tempNumberTwo=0; # the temporary number used in program
my $coordInterval=50; # every 50 time step we choose one trajectory
open INPUTFILE, "@ARGV" or die "can not open TRAJEC.xyz $!"; # open the trajectroy file. If no files, returen a warning.
@fileContent=; # open the TRAJEC.xyz file and store it into fileContent array
open OUTPUTFILE, ">>requiredTimestepsCordinates.xyz"; # open a new file to store the required coordinates.
for ($tempNumber=0;$tempNumber<5 array="" br="" elements="" five="" in="" nbsp="" read="" requiredcoordinates="" tempnumber="">
for ($tempNumberTwo=0;$tempNumberTwo<($moleculeNumberOfAtoms+$numberOfSeparation);$tempNumberTwo++) { # read 10 lines from coordinate file
## you can not skip the N.O. 0 element since all arrays have first elment with index 0.
print OUTPUTFILE $fileContent[($requiredCoordinates[$tempNumber]-1)/50*($moleculeNumberOfAtoms+$numberOfSeparation)+ $tempNumberTwo]; #
}
}
close INPUTFILE;
close OUTPUTFILE;
#! /usr/bin/perl -w
my @line=0;
my $i=0;
open FILE1, "10waterch3och3noatom.xyz" or die $!;
@line=
for ($i=0;$i<10 br="" i="">open FILE2, "> water-opart$i";
open FILE3, "> water-hpart$i";
print FILE2 $line[3*$i];
print FILE3 $line[3*$i+1];
print FILE3 $line[3*$i+2];
close FILE2;
close FILE3;
}
close FILE1;
------------------------------------------------------------------------------------------------------
std.pl
#! /usr/bin/perl -w -l
my @eksenergy=0;
my $tempnumber=0;
my $nobias_average_energy=0;
my $product_average_energy=0;
my $temptotal=0;
my $count=0;
my $energy_std=0;
my $selected_range_start=0;
my $selected_range_end=35000;
open ENERGYFILE, 'eks.dat' or die 'can not find the file!';
while (
$eksenergy[$tempnumber]=$_;
$tempnumber++;
}
close ENERGYFILE;
print 'total numbers are ', $tempnumber;
for ($count=$selected_range_start;$count<$selected_range_end; $count++){
$temptotal=$eksenergy[$count]+$temptotal;
}
$nobias_average_energy=$temptotal/($selected_range_end-$selected_range_start);
$temptotal=0;
for ($count=$selected_range_start;$count<$selected_range_end;$count++){
$temptotal=($eksenergy[$count]-$nobias_average_energy)**2+$temptotal
}
$energy_std=($temptotal/($selected_range_end-$selected_range_start))**(1/2);
print 'the STD is ', $energy_std*627.509;
print 'the average is ', $nobias_average_energy*627.509;
-----------------------------------------------------------------------------------------------------------
decide-h3.pl
#! /usr/bin/perl -w
my @line=0;
my $i=0;
open FILE1, "COLVAR" or die $!;
@line=
for ($i=0;$i<500 br="" i="">open FILE2, "> hpart$i";
print FILE2 $line[$i];
close FILE2;
}
close FILE1;
-----------------------------------------------------------------------------------------------------------
find-1214161820.pl
#! /usr/bin/perl -w
my @fileContent=0; # array to store contents of a file
my @tempStore=0; # temporary array to store data
my @requiredCoordinates=qw(120001 140001 160001 180001 200001); # get the required time-step coordinates in a TRAJECTORY file.
my $moleculeNumberOfAtoms=8; # the number of one system: methanol and oxygen
my $numberOfSeparation=2; # the separation lines between two coordinate file
my $tempNumber=0; # the temporary number used in program
my $tempNumberTwo=0; # the temporary number used in program
my $coordInterval=50; # every 50 time step we choose one trajectory
open INPUTFILE, "@ARGV" or die "can not open TRAJEC.xyz $!"; # open the trajectroy file. If no files, returen a warning.
@fileContent=
open OUTPUTFILE, ">>requiredTimestepsCordinates.xyz"; # open a new file to store the required coordinates.
for ($tempNumber=0;$tempNumber<5 array="" br="" elements="" five="" in="" nbsp="" read="" requiredcoordinates="" tempnumber="">
for ($tempNumberTwo=0;$tempNumberTwo<($moleculeNumberOfAtoms+$numberOfSeparation);$tempNumberTwo++) { # read 10 lines from coordinate file
## you can not skip the N.O. 0 element since all arrays have first elment with index 0.
print OUTPUTFILE $fileContent[($requiredCoordinates[$tempNumber]-1)/50*($moleculeNumberOfAtoms+$numberOfSeparation)+ $tempNumberTwo]; #
}
}
close INPUTFILE;
close OUTPUTFILE;
some of my perl code and bash script------I
clean.sh
rm log.file HILLS* TRAJEC* COLVAR* RESTART.1 GEO_OPT.xyz HESSIAN *.out LATEST ENERGIES GEOMETRY* input.out name*
--------------------------------------------------------------------------------------------------------------
average.pl
#! /usr/bin/perl -w
use warnings;
use strict;
my $m=0;
my $n =35000;
my $pn = 68000;
my @eks=0;
my $ksind=0;
my $reactave=0;
my $prodave=0;
my $temp=0;
open KSFILE, 'eks.dat';
while (){
$eks[$ksind]=$_+55.9;
$ksind +=1;
}
print "$eks[34999] \n";
print "the average of reactant";
for ($m=0;$m<$n;$m++){
$temp=$eks[$m]+$temp;
}
$reactave=$temp/$n*2625.5/4.18;
print "$reactave \n";
print "the average of product";
$temp=0;
$m=0;
for ($m=$pn;$m<$pn+4000;$m++){
$temp=$eks[$m]+$temp;
}
$prodave=$temp/4000*2625.5/4.18;
my $diff;
$diff= $prodave - $ reactave;
print "$prodave \n";
print "the energy difference betwen produc and reactant is ";
print "$diff \n";
--------------------------------------------------------------------------------------------
combine.sh
awk '{print $4}' ENERGIES > eks.dat
cp ~/to-gscratch/ch3oh/ch3oh-o2/01172013/nonpbc-10o2/ch3oh-oxy1/backup/ENERGIES nonpbc-energy
awk '{print $4}' nonpbc-energy > nonpbc-eks.dat
cat nonpbc-eks.dat eks.dat > eks-total.dat
---------------------------------------------------------------------------------------------
generate-zpe.pl
#! /usr/bin/perl
#!/usr/local/bin/perl
#
# change all occurances of a string in a file to another string
#
## first open a file to read all the lines
use strict;
use warnings;
my @all=0;
my @freq;
my $zpe=0;
my $m=0;
my $n=0;
my @temp;
my $newfile= "raw-freq";
my $targetfile = "freq.out";
open(MYFILE, $targetfile) or die("can not open the file freq.out");
open (OUTFILE,">", $newfile);
while () {
next unless /PURIFICATION OF DYNAMICAL MATRIX/;
$all[$m]= $_;
while ()
{
$m +=1;
$all[$m]= $_;
last if /BIG MEMORY ALLOCATIONS/;
}
}
##print @all;
##print $m;
##print $all[5];
##print $all[$m-3];
while ($n<$m-7){
@temp=split (' ', $all[$n+5]);
##print @temp;
$n +=1;
##print $n, @temp;
push (@freq,@temp);
}
foreach (@freq) {
if ($_ < 0) {
next;
}
else {
print OUTFILE "$_ \n";
$zpe=0.5*$_*4.556E-6 + $zpe;
##print "$zpe \n";
}
}
print "$zpe \n";
print OUTFILE "the ZPE is \n";
print OUTFILE $zpe;
close(MYFILE);
close (OUTFILE);
rm log.file HILLS* TRAJEC* COLVAR* RESTART.1 GEO_OPT.xyz HESSIAN *.out LATEST ENERGIES GEOMETRY* input.out name*
--------------------------------------------------------------------------------------------------------------
average.pl
#! /usr/bin/perl -w
use warnings;
use strict;
my $m=0;
my $n =35000;
my $pn = 68000;
my @eks=0;
my $ksind=0;
my $reactave=0;
my $prodave=0;
my $temp=0;
open KSFILE, 'eks.dat';
while (
$eks[$ksind]=$_+55.9;
$ksind +=1;
}
print "$eks[34999] \n";
print "the average of reactant";
for ($m=0;$m<$n;$m++){
$temp=$eks[$m]+$temp;
}
$reactave=$temp/$n*2625.5/4.18;
print "$reactave \n";
print "the average of product";
$temp=0;
$m=0;
for ($m=$pn;$m<$pn+4000;$m++){
$temp=$eks[$m]+$temp;
}
$prodave=$temp/4000*2625.5/4.18;
my $diff;
$diff= $prodave - $ reactave;
print "$prodave \n";
print "the energy difference betwen produc and reactant is ";
print "$diff \n";
--------------------------------------------------------------------------------------------
combine.sh
awk '{print $4}' ENERGIES > eks.dat
cp ~/to-gscratch/ch3oh/ch3oh-o2/01172013/nonpbc-10o2/ch3oh-oxy1/backup/ENERGIES nonpbc-energy
awk '{print $4}' nonpbc-energy > nonpbc-eks.dat
cat nonpbc-eks.dat eks.dat > eks-total.dat
---------------------------------------------------------------------------------------------
generate-zpe.pl
#! /usr/bin/perl
#!/usr/local/bin/perl
#
# change all occurances of a string in a file to another string
#
## first open a file to read all the lines
use strict;
use warnings;
my @all=0;
my @freq;
my $zpe=0;
my $m=0;
my $n=0;
my @temp;
my $newfile= "raw-freq";
my $targetfile = "freq.out";
open(MYFILE, $targetfile) or die("can not open the file freq.out");
open (OUTFILE,">", $newfile);
while (
next unless /PURIFICATION OF DYNAMICAL MATRIX/;
$all[$m]= $_;
while (
{
$m +=1;
$all[$m]= $_;
last if /BIG MEMORY ALLOCATIONS/;
}
}
##print @all;
##print $m;
##print $all[5];
##print $all[$m-3];
while ($n<$m-7){
@temp=split (' ', $all[$n+5]);
##print @temp;
$n +=1;
##print $n, @temp;
push (@freq,@temp);
}
foreach (@freq) {
if ($_ < 0) {
next;
}
else {
print OUTFILE "$_ \n";
$zpe=0.5*$_*4.556E-6 + $zpe;
##print "$zpe \n";
}
}
print "$zpe \n";
print OUTFILE "the ZPE is \n";
print OUTFILE $zpe;
close(MYFILE);
close (OUTFILE);
Tuesday, November 19, 2013
how to calculate a error bar
first, compute the average (i.e., the estimator) for your measurements, by evaluating the following formula:
average = (sample1 + sample2 + ... + sampleN) / N
Replace "sample1," sample2," ... "sampleN" by the measurements, and "N" by the total number of measurements in the experiment.
Second, compute the standard deviation by evaluating the following formula:
stdDev = sqrt(((sample1 - average)**2 + ... + (sampleN - average)**2)/N) or
stdDev = sqrt(((sample1 - average)**2 + ... + (sampleN - average)**2)/(N-1)) if two DOFs depend on each other.
Finally, compute the beginning and end points of the error bars, by evaluating the following formulas:
barBegin = average - stdDev
barEnd = average + stdDev
If you want to use gnuplot, following command is used.
average = (sample1 + sample2 + ... + sampleN) / N
Replace "sample1," sample2," ... "sampleN" by the measurements, and "N" by the total number of measurements in the experiment.
Second, compute the standard deviation by evaluating the following formula:
stdDev = sqrt(((sample1 - average)**2 + ... + (sampleN - average)**2)/N) or
stdDev = sqrt(((sample1 - average)**2 + ... + (sampleN - average)**2)/(N-1)) if two DOFs depend on each other.
Finally, compute the beginning and end points of the error bars, by evaluating the following formulas:
barBegin = average - stdDev
barEnd = average + stdDev
If you want to use gnuplot, following command is used.
plot "yourfile.txt" using 1:2:3 with yerrorbars !here 1, 2, 3 are steps, mean,and stdev, respectively or you can useplot "yourfile.txt" using 1:($2-$3):($2-$3):($2+$3):($2+$3) with candlesticks!this will generate a candlesticks. Friday, November 15, 2013
one example to use CPMD to obtain the TS state
However, it may have some problems to get converged. Maybe the energy cutoff?
The initial guess structure?
&CPMD
OPTIMIZE GEOMETRY XYZ
INITIALIZE WAVEFUNCTIONS ATOMS
RANDOMIZE COORDINATES
0.1D0
RESTFILE
4
STORE
100
LBFGS
PRFO MODE
10
PRFO CORE=4
1 2 9 10
CONVERGENCE
5.0D-7 5.0D-5
CONVERGENCE RELAX
15
SPLINE POINTS QFUNCTION
2001
ISOLATED MOLECULE
CENTER MOLECULE OFF
MEMORY BIG
LSD
&END
&DFT
FUNCTIONAL PBE
GC-CUTOFF
5.0D-5
&END
&SYSTEM
SYMMETRY
0
POISSON SOLVER TUCKERMAN
ANGSTROM
CELL
10.0D0 1.0D0 1.0D0 0.0D0 0.0D0 0.0D0
CUTOFF
25.0D0
MULTIPLICITY
1
&END
&ATOMS
*N.uspp_ascii FORMATTED
LMAX=P
2
4.525338176055 4.920747785642 4.949904563339
5.765416638683 5.048851794396 5.079925564279
*H.uspp_ascii FORMATTED
LMAX=S
6
4.265466440716 2.788011128505 4.858413782037
2.878604693260 3.791408955331 4.306112314885
4.333398001463 3.598265838244 3.267273093363
6.467823612522 3.016976904998 5.093103687689
6.554809448253 3.823511424486 3.501228774397
7.703325625270 4.291321957329 4.803526469019
*C.uspp_ascii FORMATTED
LMAX=P
2
3.972567677301 3.700817361171 4.307476081948
6.672717274443 3.979768413937 4.589493362517
&END
Tuesday, November 12, 2013
Plumed utility usage: sum_hills and HILLS file
parallel.f90 serial.f90 sum_hills.f90 files are avaialble.
I use module to link library. In the following part, s denotes step. It seems that gcc is better.
s1: module load gcc_4.4.7-ompi_1.6.5 (module list, module load, module avail, module unload)
s2: mpif90 -O3 sum_hills.f90 parallel.f90 -o sum_hills_mpi.x
You should have sum_hills_mpi.x generated.s3. ldd sum_hills_mpi.x
Output:
linux-vdso.so.1 => (0x00007fff205fd000)
libmpi_f90.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi_f90.so.1 (0x00002b18668f0000)
libmpi_f77.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi_f77.so.1 (0x00002b1866af5000)
libmpi.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi.so.1 (0x00002b1866d28000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b18670d9000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00002b18672de000)
libm.so.6 => /lib64/libm.so.6 (0x00002b18675d0000)
libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00002b1867853000)
librt.so.1 => /lib64/librt.so.1 (0x00002b1867a59000)
libnsl.so.1 => /lib64/libnsl.so.1 (0x00002b1867c62000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002b1867e7a000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b186807e000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b186828c000)
libc.so.6 => /lib64/libc.so.6 (0x00002b18684a8000)
/lib64/ld-linux-x86-64.so.2 (0x00002b18666d2000)
s4: gfortran -O3 sum_hills.f90 serial.f90 -o sum_hills.x !OK. now serial version.
s5: copy two *.x files to your bin directory.
s6. sum_hills.x -file HILLS -out fes.dat -ndim 3 -ndw 1 2 -kt 0.6 -ngrid 100 100 100
-ndim: the dimensionality number.
-ndw: the list of CVs in the desired order to plot the FES.
-kt: KT specified by -kt (kT must be given in the energy units that were used
by in the code)
HILLS file
first column second third fourth
time step CV SIGMA Bias potential
I use module to link library. In the following part, s denotes step. It seems that gcc is better.
s1: module load gcc_4.4.7-ompi_1.6.5 (module list, module load, module avail, module unload)
s2: mpif90 -O3 sum_hills.f90 parallel.f90 -o sum_hills_mpi.x
You should have sum_hills_mpi.x generated.s3. ldd sum_hills_mpi.x
Output:
linux-vdso.so.1 => (0x00007fff205fd000)
libmpi_f90.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi_f90.so.1 (0x00002b18668f0000)
libmpi_f77.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi_f77.so.1 (0x00002b1866af5000)
libmpi.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi.so.1 (0x00002b1866d28000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b18670d9000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00002b18672de000)
libm.so.6 => /lib64/libm.so.6 (0x00002b18675d0000)
libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00002b1867853000)
librt.so.1 => /lib64/librt.so.1 (0x00002b1867a59000)
libnsl.so.1 => /lib64/libnsl.so.1 (0x00002b1867c62000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002b1867e7a000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b186807e000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b186828c000)
libc.so.6 => /lib64/libc.so.6 (0x00002b18684a8000)
/lib64/ld-linux-x86-64.so.2 (0x00002b18666d2000)
s4: gfortran -O3 sum_hills.f90 serial.f90 -o sum_hills.x !OK. now serial version.
s5: copy two *.x files to your bin directory.
s6. sum_hills.x -file HILLS -out fes.dat -ndim 3 -ndw 1 2 -kt 0.6 -ngrid 100 100 100
-ndim: the dimensionality number.
-ndw: the list of CVs in the desired order to plot the FES.
-kt: KT specified by -kt (kT must be given in the energy units that were used
by in the code)
HILLS file
first column second third fourth
time step CV SIGMA Bias potential
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