Started adding tests on PLUMED interface

#!/bin/bash

# Check PLUMED positions

nlines=`paste plumed.xyz lammps.xyz | awk '{if( $2<$6-0.0001 || $2>$6+0.0001 || $3<$7-0.0001 || $3>$7+0.0001 || $4<$8-0.0002 || $4>$8+0.0002 ) if( $5!="Timestep:" && $1!=2004 ) print $0}' | wc -l` 

if [ "$nlines" -gt 0 ] ; then

   echo ERROR passing positions from LAMMPS to PLUMED

   paste plumed.xyz lammps.xyz | awk '{if( $2<$6-0.0001 || $2>$6+0.0001 || $3<$7-0.0001 || $3>$7+0.0001 || $4<$8-0.0002 || $4>$8+0.0002 ) if( $5!="Timestep:" && $1!=2004 ) print $0, $2-$6, $3-$7, $4-$8}'

fi

# CHECK PLUMED timestep

tstep=`grep timestep in.peptide-plumed | awk '{print $2}'`

tstep=`echo $tstep \* 0.001 \* 10 | bc -l`

nlines=`wc -l plmd_energy | awk '{print $1}'`

for ((i=3;i<$nlines;i++)); do

   told=`head -n $(($i-1)) plmd_energy | tail -n 1 | awk '{print $1}'`

   tnew=`head -n $i plmd_energy | tail -n 1 | awk '{print $1}'`

   tdiff=`echo \( $tnew - $told - $tstep \) \> 0 | bc -l`

   if [ $tdiff -gt 0 ] ; then

      echo ERROR passing timestep from LAMMPS to PLUMED

   fi

done

# Check PLUMED energy

tail -n +2 plmd_energy > plmd_energy2 

nlines=`paste lammps_energy plmd_energy2 | tail -n +2 | awk '{if( $2<$4-0.0001 || $2>$4+0.0001 ) print $0}' | wc -l` 

if [ "$nlines" -gt 0 ] ; then

   echo ERROR passing potential energy from LAMMPS to PLUMED

   paste lammps_energy plmd_energy2 | tail -n +2 | awk '{if( $2<$4-0.0001 || $2>$4+0.0001 ) print $0}'

fi

rm -f plmd_energy2

#! FIELDS time d1 d2 h_pot.bias h_pot.force2

 0.000000 0.993491 0.758366 0.292146 5.842921

 0.002000 0.995476 0.759311 0.289757 5.795146

 0.004000 0.997617 0.760436 0.286982 5.739638

 0.006000 0.999849 0.761714 0.283902 5.678045

 0.008000 1.002126 0.763111 0.280604 5.612077

 0.010000 1.004429 0.764614 0.277132 5.542631

 0.012000 1.006758 0.766228 0.273476 5.469523

 0.014000 1.009119 0.767975 0.269594 5.391885

 0.016000 1.011514 0.769873 0.265455 5.309099

 0.018000 1.013929 0.771911 0.261093 5.221860

 0.020000 1.016331 0.774032 0.256641 5.132826

 0.022000 1.018671 0.776135 0.252321 5.046430

 0.024000 1.020900 0.778094 0.248395 4.967894

 0.026000 1.022979 0.779791 0.245099 4.901982

 0.028000 1.024903 0.781143 0.242592 4.851832

 0.030000 1.026700 0.782129 0.240904 4.818078

 0.032000 1.028430 0.782795 0.239931 4.798623

 0.034000 1.030167 0.783248 0.239458 4.789166

 0.036000 1.031975 0.783621 0.239212 4.784241

 0.038000 1.033897 0.784047 0.238923 4.778459

 0.040000 1.035930 0.784627 0.238382 4.767647

 0.042000 1.038033 0.785407 0.237484 4.749678

 0.044000 1.040121 0.786369 0.236240 4.724809

 0.046000 1.042091 0.787439 0.234768 4.695368

 0.048000 1.043837 0.788511 0.233246 4.664919

 0.050000 1.045280 0.789471 0.231863 4.637266

 0.052000 1.046388 0.790226 0.230785 4.615694

 0.054000 1.047178 0.790712 0.230136 4.602723

 0.056000 1.047712 0.790891 0.230015 4.600302

 0.058000 1.048083 0.790742 0.230505 4.610102

 0.060000 1.048397 0.790252 0.231683 4.633662

 0.062000 1.048754 0.789414 0.233618 4.672352

 0.064000 1.049236 0.788230 0.236354 4.727083

 0.066000 1.049892 0.786723 0.239883 4.797654

 0.068000 1.050741 0.784954 0.244096 4.881918

 0.070000 1.051768 0.783036 0.248766 4.975312

 0.072000 1.052946 0.781120 0.253559 5.071179

 0.074000 1.054246 0.779374 0.258094 5.161873

 0.076000 1.055648 0.777949 0.262017 5.240331

 0.078000 1.057143 0.776950 0.265083 5.301665

 0.080000 1.058728 0.776406 0.267217 5.344336

 0.082000 1.060397 0.776265 0.268526 5.370525

 0.084000 1.062135 0.776403 0.269282 5.385630

 0.086000 1.063918 0.776650 0.269855 5.397095

 0.088000 1.065713 0.776818 0.270642 5.412845

 0.090000 1.067486 0.776746 0.271982 5.439646

 0.092000 1.069203 0.776331 0.274084 5.481685

 0.094000 1.070839 0.775547 0.276987 5.539735

 0.096000 1.072370 0.774448 0.280554 5.611090

 0.098000 1.073779 0.773153 0.284514 5.690279

 0.100000 1.075049 0.771810 0.288515 5.770295

 0.102000 1.076167 0.770572 0.292193 5.843867

 0.104000 1.077116 0.769571 0.295223 5.904455

 0.106000 1.077882 0.768908 0.297345 5.946904

 0.108000 1.078459 0.768648 0.298397 5.967949

 0.110000 1.078853 0.768806 0.298342 5.966843

 0.112000 1.079090 0.769340 0.297296 5.945926

 0.114000 1.079219 0.770158 0.295516 5.910315

 0.116000 1.079303 0.771141 0.293328 5.866561

 0.118000 1.079415 0.772170 0.291067 5.821338

 0.120000 1.079622 0.773135 0.289037 5.780735

 0.122000 1.079971 0.773942 0.287489 5.749783

 0.124000 1.080476 0.774515 0.286599 5.731971

 0.126000 1.081103 0.774812 0.286437 5.728730

 0.128000 1.081783 0.774828 0.286955 5.739101

 0.130000 1.082421 0.774602 0.287987 5.759744

 0.132000 1.082925 0.774217 0.289271 5.785430

 0.134000 1.083230 0.773787 0.290498 5.809961

 0.136000 1.083320 0.773437 0.291366 5.827324

 0.138000 1.083229 0.773283 0.291638 5.832753

 0.140000 1.083032 0.773417 0.291171 5.823427

 0.142000 1.082825 0.773886 0.289936 5.798729

 0.144000 1.082697 0.774694 0.288007 5.760150

 0.146000 1.082716 0.775795 0.285550 5.710997

 0.148000 1.082911 0.777098 0.282797 5.655945

 0.150000 1.083267 0.778482 0.280018 5.600355

 0.152000 1.083739 0.779816 0.277467 5.549332

 0.154000 1.084258 0.780984 0.275337 5.506735

 0.156000 1.084764 0.781917 0.273726 5.474524

 0.158000 1.085215 0.782595 0.272633 5.452651

 0.160000 1.085600 0.783050 0.271973 5.439463

 0.162000 1.085939 0.783349 0.271614 5.432288

 0.164000 1.086269 0.783582 0.271395 5.427907

 0.166000 1.086632 0.783845 0.271141 5.422814

 0.168000 1.087062 0.784236 0.270670 5.413403

 0.170000 1.087575 0.784841 0.269815 5.396302

 0.172000 1.088169 0.785721 0.268447 5.368936

 0.174000 1.088827 0.786902 0.266506 5.330122

 0.176000 1.089527 0.788366 0.264020 5.280397

 0.178000 1.090249 0.790062 0.261095 5.221908

 0.180000 1.090983 0.791909 0.257899 5.157988

 0.182000 1.091725 0.793812 0.254634 5.092674

 0.184000 1.092478 0.795671 0.251513 5.030265

 0.186000 1.093252 0.797384 0.248746 4.974922

 0.188000 1.094056 0.798864 0.246512 4.930235

 0.190000 1.094906 0.800048 0.244938 4.898769

 0.192000 1.095809 0.800909 0.244083 4.881658

 0.194000 1.096763 0.801455 0.243917 4.878336

 0.196000 1.097747 0.801731 0.244326 4.886516

 0.198000 1.098716 0.801809 0.245123 4.902456

 0.200000 1.099614 0.801777 0.246077 4.921541

thermo_style	custom step temp etotal pe ke epair ebond f_2

thermo		10

dump            dd all xyz 10 lammps.xyz

variable        step equal step

variable        pe equal pe

fix             5 all print 10 "$(v_step) $(v_pe)" file lammps_energy

run		100

run		101

PLUMED: PLUMED is starting

PLUMED: Version: 2.5.0-dev (git: a10584333) compiled on Jul  2 2018 at 09:29:02

PLUMED: Please cite this paper when using PLUMED [1]

PLUMED: For further information see the PLUMED web page at http://www.plumed.org

PLUMED: Root: /data/gt/mycodes/plumed2/

PLUMED: For installed feature, see /data/gt/mycodes/plumed2//src/config/config.txt

PLUMED: Molecular dynamics engine: LAMMPS

PLUMED: Precision of reals: 8

PLUMED: Running over 1 node

PLUMED: Number of threads: 1

PLUMED: Cache line size: 512

PLUMED: Number of atoms: 2004

PLUMED: File suffix: 

PLUMED: FILE: plumed.dat

PLUMED: Action COM

PLUMED:   with label c1

PLUMED:   serial associated to this virtual atom is 2005

PLUMED:   of atoms

PLUMED:  2 4 5 6

PLUMED:   broken molecules will be rebuilt assuming atoms are in the proper order

PLUMED: Action COM

PLUMED:   with label c2

PLUMED:   serial associated to this virtual atom is 2006

PLUMED:   of atoms

PLUMED:  80 82 83 84

PLUMED:   broken molecules will be rebuilt assuming atoms are in the proper order

PLUMED: Action DISTANCE

PLUMED:   with label d1

PLUMED:   between atoms 2005 37

PLUMED:   using periodic boundary conditions

PLUMED: Action DISTANCE

PLUMED:   with label d2

PLUMED:   between atoms 2006 37

PLUMED:   using periodic boundary conditions

PLUMED: Action RESTRAINT

PLUMED:   with label h_pot

PLUMED:   with arguments d1 d2

PLUMED:   added component to this action:  h_pot.bias 

PLUMED:   at 1.000000 1.000000

PLUMED:   with harmonic force constant 10.000000 10.000000

PLUMED:   and linear force constant 0.000000 0.000000

PLUMED:   added component to this action:  h_pot.force2 

PLUMED: Action PRINT

PLUMED:   with label @5

PLUMED:   with stride 1

PLUMED:   with arguments d1 d2 h_pot.bias h_pot.force2

PLUMED:   on file colvar

PLUMED:   with format  %f

PLUMED: END FILE: plumed.dat

PLUMED: Timestep: 0.002000

PLUMED: KbT has not been set by the MD engine

PLUMED: It should be set by hand where needed

PLUMED: Relevant bibliography:

PLUMED:   [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)

PLUMED: Please read and cite where appropriate!

PLUMED: Finished setup

PLUMED:                                               Cycles        Total      Average      Minumum      Maximum

PLUMED:                                                    1     0.015035     0.015035     0.015035     0.015035

PLUMED: 1 Prepare dependencies                           101     0.000123     0.000001     0.000001     0.000004

PLUMED: 2 Sharing data                                   101     0.006837     0.000068     0.000047     0.000891

PLUMED: 3 Waiting for data                               101     0.000967     0.000010     0.000007     0.000041

PLUMED: 4 Calculating (forward loop)                     101     0.001616     0.000016     0.000011     0.000043

PLUMED: 5 Applying (backward loop)                       101     0.002159     0.000021     0.000018     0.000057

PLUMED: 6 Update                                         101     0.001059     0.000010     0.000006     0.000086

UNITS ENERGY=kcal/mol

c1: COM ATOMS=2,4,5,6

c2: COM ATOMS=80,82,83,84

d1: DISTANCE ATOMS=c1,37

d2: DISTANCE ATOMS=c2,37

h_pot: RESTRAINT ARG=d1,d2 AT=1.0,1.0 KAPPA=10,10

PRINT ARG=d1,d2,h_pot.* FILE=colvar

energy: ENERGY

DUMPATOMS ATOMS=1-2004 FILE=plumed.xyz UNITS=A PRECISION=4 STRIDE=10

PRINT ARG=energy STRIDE=10 FMT=%8.4f FILE=plmd_energy