Example: Trajectory replays for PES scans, NEB and MD calculations¶
#!/bin/sh
# 1. Replay of PES scans
# ======================
AMS_JOBNAME=pesscan "$AMSBIN/ams" << eor
Task PESScan
PESScan
ScanCoordinate
nPoints 6
Dihedral 5 1 2 6 0.0 50
Dihedral 4 1 2 3 0.0 50
End
ScanCoordinate
nPoints 7
Distance 1 2 1.2 1.5
End
End
System
Atoms
C 0.0 -0.0 0.66687
C 0.0 -0.0 -0.33313
H 0.0 0.92974 -0.90538
H 0.0 0.92974 1.23912
H 0.0 -0.92974 1.23912
H 0.0 -0.92974 -0.90538
End
End
Engine ForceField
EndEngine
eor
AMS_JOBNAME=replay_pesscan "$AMSBIN/ams" << eor
Task Replay
Replay
File pesscan.results
StoreAllResultFiles Yes
End
Properties
Gradients True
End
Engine DFTB
EndEngine
eor
echo "Start extracting data from ams.rkf ..."
echo "Number of frames on file:"
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'History%nEntries'
frame=1
while [ $frame -le 42 ]; do
echo "Frame: $frame"
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r "History%Energy($frame)"
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r "History%Gradients($frame)"
frame=$(expr $frame + 1)
done
echo "Data in PESScan section:"
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'PESScan%PESCoords'
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'PESScan%PES'
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'PESScan%HistoryIndices'
echo "Data extracted."
# 2. Replay of NEB calculations
# =============================
AMS_JOBNAME=neb "$AMSBIN/ams" << eor
Task NEB
NEB
Images 16
End
GeometryOptimization
Convergence
Energy 1.0e-4
Gradients 1.0e-2
End
End
System
Atoms
C -0.04837097189972882 0.002828754545985427 1.099927275387085
C -0.7231327687579711 -1.264630955508361 1.591341080262239
C -0.7174118987979032 1.275587203448819 1.585489846719994
H -1.758221225827696 -1.294861009536393 1.215612210647893
H -0.7536609466556244 -1.286949469754588 2.689737906089842
H 0.02700743800283175 0.0001348498227195367 0.004547638456250216
H -0.7481941882345999 1.302956664081095 2.683766567353197
H -0.1880537663322776 2.167332127899618 1.228056629315197
H -1.752232117403696 1.308927696210993 1.209290912745431
H -0.1979764470101184 -2.160385916691095 1.237731888775011
Cl 1.710726893919094 4.005547128448699e-05 1.649098041095717
End
End
System final
Atoms
C -0.8173023574499557 -0.01408167289928656 0.8544841004283144
C -1.086263680920393 -1.14724517989661 1.518039806717775
C -0.8990221290639472 1.362120508644236 1.43231282384412
H -1.018446188967536 -2.121649215821082 1.03173453221026
H -1.404982357822256 -1.129945575549278 2.563696578967125
H -0.5085933307712909 -0.08344191227560969 -0.1948268157146379
H -1.210244367762068 1.342173382164807 2.485525533439326
H 0.07413947140246446 1.873805664554979 1.364278897383801
H -1.616521025856608 1.9769362830809 0.8657976784252567
H 1.044986335480545 -0.9543604705303219 1.922869894354733
Cl 2.292729632733364 -1.053331811482705 2.350686966791855
End
End
Engine DFTB
EndEngine
eor
AMS_JOBNAME=replay_neb "$AMSBIN/ams" << eor
Task Replay
Replay File=neb.results/ams.rkf
Engine ADF
NumericalQuality Basic
EndEngine
eor
echo "Start extracting data from ams.rkf ..."
echo "Number of frames on file:"
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'History%nEntries'
frame=1
while [ $frame -le 16 ]; do
echo "Frame: $frame"
$AMSBIN/amsreport replay_neb.results/ams.rkf -r "History%Energy($frame)"
frame=$(expr $frame + 1)
done
echo "Data in NEB section:"
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%nebIterations'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%historyIndex@dim'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%historyIndex'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%energy'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%highestIndex'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%LeftBarrier'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%RightBarrier'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%ReactionEnergy'
echo "Data extracted."
# 3. Replay of generic history (e.g. MD)
# ======================================
AMS_JOBNAME=md "$AMSBIN/ams" << eor
Task MolecularDynamics
MolecularDynamics
nSteps 1000
InitialVelocities Type=Zero
Trajectory SamplingFreq=10
End
System
Atoms
O 5.84400000 0.31970000 0.89540000
H 1.17000000 0.12750000 -2.13090000
H -0.61000000 -1.28280000 -1.84810000
H -0.57930000 -0.70680000 1.15800000
C -3.12520000 0.09550000 0.94430000
C -3.19980000 -1.42460000 1.23360000
C -2.05280000 0.23760000 -0.14210000
C -1.27100000 1.53130000 -0.13370000
C -0.13080000 1.46490000 -1.14670000
C -2.05030000 -2.08490000 0.42320000
C -1.08120000 -0.91390000 0.20520000
C 0.72590000 0.20890000 -1.09890000
C -0.07070000 -1.07000000 -0.90020000
C 1.91880000 0.37840000 -0.17010000
C 2.85070000 1.44940000 -0.76420000
C 4.06090000 1.66070000 0.14280000
C 0.79940000 -2.27110000 -0.66800000
C 2.70610000 -0.90160000 -0.05510000
C 4.70630000 0.33980000 0.46480000
C 2.06470000 -2.18950000 -0.28730000
C 4.02370000 -0.86790000 0.26480000
C 1.49560000 0.82380000 1.22970000
C -2.72010000 0.03450000 -1.50220000
C -4.44990000 0.59620000 0.43260000
O -5.21170000 -0.16370000 -0.11570000
C -4.82510000 2.04560000 0.60460000
H -2.82710000 0.64000000 1.83720000
H -3.05600000 -1.60950000 2.29900000
H -4.16120000 -1.82340000 0.91220000
H -1.95080000 2.35390000 -0.41170000
H -0.90510000 1.74180000 0.87040000
H -0.54560000 1.56290000 -2.16020000
H 0.51310000 2.34310000 -1.00320000
H -1.56740000 -2.86790000 1.01220000
H -2.40770000 -2.48600000 -0.52040000
H 3.18420000 1.11610000 -1.74960000
H 2.30420000 2.38610000 -0.86930000
H 4.79290000 2.28810000 -0.38330000
H 3.77550000 2.17310000 1.05860000
H 0.36740000 -3.25490000 -0.82120000
H 2.63690000 -3.09890000 -0.14660000
H 4.55990000 -1.80060000 0.37040000
H 0.83020000 0.07700000 1.66290000
H 2.37890000 0.93230000 1.85900000
H 0.97580000 1.77970000 1.16520000
H -3.42010000 0.84890000 -1.68870000
H -1.95890000 0.02380000 -2.28240000
H -3.25700000 -0.91410000 -1.50550000
H -4.48270000 2.61460000 -0.25970000
H -5.90820000 2.13270000 0.69120000
H -4.35580000 2.43770000 1.50690000
End
End
Engine ReaxFF
ForceField CHON-2019.ff
EndEngine
eor
AMS_JOBNAME=replay_md "$AMSBIN/ams" << eor
Task Replay
Replay
File md.results/
Frames 1:101:10
End
Properties
Gradients True
BondOrders True
End
Engine DFTB
EndEngine
eor
echo "Start extracting data from ams.rkf ..."
echo "Number of frames on file:"
$AMSBIN/amsreport replay_md.results/ams.rkf -r 'History%nEntries'
frame=1
while [ $frame -le 11 ]; do
echo "Frame: $frame"
$AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Energy($frame)"
$AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Bonds.Index($frame)"
$AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Bonds.Atoms($frame)"
$AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Bonds.Orders($frame)#8.2f"
frame=$(expr $frame + 1)
done
echo "Data extracted."