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Tidied up example directory for PLUMED

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This commit is contained in:
Gareth Tribello
2018-07-12 16:22:40 +01:00
parent 6d9face1ec
commit c442166ded
18 changed files with 164 additions and 379 deletions
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89
examples/USER/plumed/check-plumed.sh
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# Needs make yes-molecule
# make yes-rigid
# make yes-kspace
# make yes-user-plumed ( obviously )
#!/bin/bash
LAMMPS=../../../src/lmp_mpi
# Run first LAMMPS calculation
$LAMMPS < in.peptide-plumed
# 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
# Check PLMD mass and charge
nlines=`wc -l mq_lammps | awk '{print $1}'`
sline=`grep -n "mass q" mq_lammps | awk '{print $1}' | sed -e s/:ITEM://`
for ((i=$sline+1;i<$nlines;i++)); do
# Mass and charge from LAMMPS
index=`head -n $i mq_lammps | tail -n 1 | awk '{print $1}'`
l_mass=`head -n $i mq_lammps | tail -n 1 | awk '{print $2}'`
l_charge=`head -n $i mq_lammps | tail -n 1 | awk '{print $3}'`
# Mass and charge from PLUMED
p_mass=`head -n $(($index+1)) mq_plumed | tail -n 1 | awk '{print $2}'`
p_charge=`head -n $(($index+1)) mq_plumed | tail -n 1 | awk '{print $3}'`
# Check PLUMED mass is same as lammps mass
mdiff=`echo \( $l_mass - $p_mass \) \> 0 | bc -l`
if [ "$mdiff" -gt 0 ] ; then
echo ERROR passing masses from LAMMPS to PLUMED
fi
# Check PLUMED charge is same as lammps charge
qdiff=`echo \( $l_charge - $p_charge \) \> 0 | bc -l`
if [ "$qdiff" -gt 0 ] ; then
echo ERROR passing charges from LAMMPS to PLUMED
fi
done
# Run calculations to test adding restraint on bond
$LAMMPS < in.peptide-plumed-plumed-restraint
$LAMMPS < in.peptide-plumed-lammps-restraint
# Now compare value of distance when lammps and plumed restraint the distance
nlines=`paste lammps_restraint plumed_restraint | 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 forces from PLUMED back to LAMMPS
fi
# Now run calculations to test virial
$LAMMPS < in.peptide-plumed-npt
$LAMMPS < in.peptide-plumed-npt2
nlines=`paste plmd_volume_with_restraint plmd_volume_without_restraint | 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 virial from PLUMED back to LAMMPS
fi
# Nothing from here works
# Now run calculations to check forces on energy
$LAMMPS < in.peptide-plumed-engforce-ref
$LAMMPS < in.peptide-plumed-eng-force-plumed

8
examples/USER/plumed/clear-files.sh
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#!/bin/bash
# Data from first set of checks
rm bck.* plmd_energy lammps_energy mq_plumed mq_lammps lammps.xyz plumed.xyz p.log
# Data from checks on restraints
rm bck.* p.log lammps_restraint plumed_restraint
# Data from checks on virial
rm bck.* lammps_energy lammps.xyz log.lammps plmd_volume p.log plmd_volume_without_restraint plmd_volume_with_restraint

103
examples/USER/plumed/colvar Normal file
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#! FIELDS time dd
0.000000 5.985554
0.002000 6.002880
0.004000 6.022015
0.006000 6.029922
0.008000 6.020103
0.010000 5.996906
0.012000 5.972734
0.014000 5.960079
0.016000 5.963714
0.018000 5.978140
0.020000 5.991813
0.022000 5.995155
0.024000 5.987021
0.026000 5.975340
0.028000 5.971456
0.030000 5.981945
0.032000 6.003550
0.034000 6.024743
0.036000 6.032990
0.038000 6.022936
0.040000 6.000131
0.042000 5.977800
0.044000 5.968692
0.046000 5.977224
0.048000 5.996934
0.050000 6.014800
0.052000 6.019586
0.054000 6.008803
0.056000 5.989809
0.058000 5.974484
0.060000 5.971140
0.062000 5.979074
0.064000 5.989379
0.066000 5.991356
0.068000 5.980176
0.070000 5.960625
0.072000 5.944401
0.074000 5.942614
0.076000 5.958402
0.078000 5.984574
0.080000 6.007964
0.082000 6.017667
0.084000 6.011795
0.086000 5.998304
0.088000 5.989405
0.090000 5.993275
0.092000 6.008545
0.094000 6.025183
0.096000 6.031186
0.098000 6.020651
0.100000 5.997952
0.102000 5.975230
0.104000 5.964757
0.106000 5.971150
0.108000 5.988568
0.110000 6.004676
0.112000 6.008731
0.114000 5.998481
0.116000 5.981406
0.118000 5.969615
0.120000 5.971827
0.122000 5.987658
0.124000 6.007888
0.126000 6.020477
0.128000 6.018377
0.130000 6.004046
0.132000 5.987682
0.134000 5.980338
0.136000 5.986534
0.138000 6.001303
0.140000 6.013589
0.142000 6.013717
0.144000 6.000028
0.146000 5.980283
0.148000 5.966836
0.150000 5.968670
0.152000 5.985459
0.154000 6.007612
0.156000 6.022374
0.158000 6.022034
0.160000 6.008851
0.162000 5.993355
0.164000 5.987212
0.166000 5.995452
0.168000 6.013111
0.170000 6.028386
0.172000 6.030387
0.174000 6.016468
0.176000 5.994191
0.178000 5.976616
0.180000 5.973983
0.182000 5.987185
0.184000 6.007275
0.186000 6.021338
0.188000 6.020837
0.190000 6.006955
0.192000 5.989433
0.194000 5.979796
0.196000 5.983601
0.198000 5.996921
0.200000 6.009310
0.202000 6.011114

3
examples/USER/plumed/in.peptide-plumed
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@ -35,10 +35,7 @@ fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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
dump mq all custom 200 mq_lammps id mass q
run 101

41
examples/USER/plumed/in.peptide-plumed-eng-force-plumed
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@ -1,41 +0,0 @@
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5
timestep 1.8181818181818181
group peptide type <= 12
group one id 2 4 5 6
group two id 80 82 83 84
group ref id 37
group colvar union one two ref
fix 1 all nvt temp 363.0 363.0 90.90909090909091 tchain 1
fix 2 all plumed plumedfile plumed-engforce.dat outfile p.log
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
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
dump mq all custom 200 mq_lammps id mass q
run 101

40
examples/USER/plumed/in.peptide-plumed-engforce-ref
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@ -1,40 +0,0 @@
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
group one id 2 4 5 6
group two id 80 82 83 84
group ref id 37
group colvar union one two ref
fix 1 all nvt temp 300.0 300.0 100.0 tchain 1
fix 2 all plumed plumedfile plumed-eng-ref.dat outfile p.log
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
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
dump mq all custom 200 mq_lammps id mass q
run 101

44
examples/USER/plumed/in.peptide-plumed-lammps-restraint
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@ -1,44 +0,0 @@
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
group one id 2 4 5 6
group two id 80 82 83 84
group ref id 37
group colvar union one two ref
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 6 all restrain bond 45 48 1000.0 1000.0 6.0
fix 2 all plumed plumedfile plumed-norestraint.dat outfile p.log
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
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
dump mq all custom 200 mq_lammps id mass q
run 101

43
examples/USER/plumed/in.peptide-plumed-npt
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@ -1,43 +0,0 @@
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
group one id 2 4 5 6
group two id 80 82 83 84
group ref id 37
group colvar union one two ref
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
fix 1 all npt temp 275.0 275.0 100.0 iso 0.987 0.987 400.0 tchain 1
fix 2 all plumed plumedfile plumed_npt.dat outfile p.log
fix 2a ref setforce 0.0 0.0 0.0
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
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
dump mq all custom 200 mq_lammps id mass q
run 101

43
examples/USER/plumed/in.peptide-plumed-npt2
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@ -1,43 +0,0 @@
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
group one id 2 4 5 6
group two id 80 82 83 84
group ref id 37
group colvar union one two ref
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
fix 1 all npt temp 275.0 275.0 100.0 iso 987.9 987.9 400.0 tchain 1
fix 2 all plumed plumedfile plumed_npt2.dat outfile p.log
fix 2a ref setforce 0.0 0.0 0.0
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
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
dump mq all custom 200 mq_lammps id mass q
run 101

44
examples/USER/plumed/in.peptide-plumed-plumed-restraint
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@ -1,44 +0,0 @@
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
group one id 2 4 5 6
group two id 80 82 83 84
group ref id 37
group colvar union one two ref
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all plumed plumedfile plumed-restraint.dat outfile p.log
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
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
dump mq all custom 200 mq_lammps id mass q
run 101

57
examples/USER/plumed/p.log Normal file
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@ -0,0 +1,57 @@
PLUMED: PLUMED is starting
PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03
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: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/
PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//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 UNITS
PLUMED: with label @0
PLUMED: length: A
PLUMED: energy: kcal/mol
PLUMED: time: ps
PLUMED: charge: e
PLUMED: mass: amu
PLUMED: using physical units
PLUMED: inside PLUMED, Boltzmann constant is 0.001987
PLUMED: Action DISTANCE
PLUMED: with label dd
PLUMED: between atoms 45 48
PLUMED: using periodic boundary conditions
PLUMED: Action RESTRAINT
PLUMED: with label @2
PLUMED: with arguments dd
PLUMED: added component to this action: @2.bias
PLUMED: at 6.000000
PLUMED: with harmonic force constant 2000.000000
PLUMED: and linear force constant 0.000000
PLUMED: added component to this action: @2.force2
PLUMED: Action PRINT
PLUMED: with label @3
PLUMED: with stride 1
PLUMED: with arguments dd
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 0.020354 0.020354 0.020354 0.020354
PLUMED: 1 Prepare dependencies 102 0.000256 0.000003 0.000001 0.000006
PLUMED: 2 Sharing data 102 0.010002 0.000098 0.000078 0.000546
PLUMED: 3 Waiting for data 102 0.001398 0.000014 0.000011 0.000072
PLUMED: 4 Calculating (forward loop) 102 0.001797 0.000018 0.000013 0.000058
PLUMED: 5 Applying (backward loop) 102 0.002666 0.000026 0.000022 0.000062
PLUMED: 6 Update 102 0.001126 0.000011 0.000007 0.000055

2
examples/USER/plumed/plumed-eng-ref.dat
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@ -1,2 +0,0 @@
e: ENERGY
PRINT ARG=e FILE=energy_ref FMT=%8.4f

3
examples/USER/plumed/plumed-engforce.dat
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@ -1,3 +0,0 @@
e: ENERGY
RESTRAINT ARG=e AT=0 SLOPE=0.1
PRINT ARG=e FILE=engforced FMT=%8.4f

3
examples/USER/plumed/plumed-norestraint.dat
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@ -1,3 +0,0 @@
UNITS LENGTH=A
dd: DISTANCE ATOMS=45,48
PRINT ARG=dd FILE=lammps_restraint FMT=%8.4f

4
examples/USER/plumed/plumed-restraint.dat
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@ -1,4 +0,0 @@
UNITS LENGTH=A ENERGY=kcal/mol
dd: DISTANCE ATOMS=45,48
RESTRAINT ARG=dd KAPPA=2000 AT=6.0
PRINT ARG=dd FILE=plumed_restraint FMT=%8.4f

11
examples/USER/plumed/plumed.dat
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@ -1,7 +1,4 @@
UNITS ENERGY=kcal/mol
c1: COM ATOMS=2,4,5,6
c2: COM ATOMS=80,82,83,84
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
DUMPMASSCHARGE FILE=mq_plumed
UNITS LENGTH=A ENERGY=kcal/mol
dd: DISTANCE ATOMS=45,48
RESTRAINT ARG=dd KAPPA=2000 AT=6.0
PRINT ARG=dd FILE=colvar

2
examples/USER/plumed/plumed_npt.dat
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@ -1,2 +0,0 @@
vv: VOLUME
PRINT ARG=vv FILE=plmd_volume_without_restraint FMT=%8.5f

3
examples/USER/plumed/plumed_npt2.dat
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@ -1,3 +0,0 @@
vv: VOLUME
RESTRAINT AT=0.0 ARG=vv SLOPE=-60.221429
PRINT ARG=vv FILE=plmd_volume_with_restraint FMT=%8.5f