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LASP Tutorial Xiamen AIworkshop 2019
LASP Tutorial Xiamen AIworkshop 2019
Tutorial
Cheng Shang, Zhipan Liu
Department of Chemistry, Fudan University
Shanghai, China
LaSpHUB Large-scale Atomic Simulation with neural network Potential
Content:
What is LASP
How to get
How to compile
How to run
How to discuss
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What is LASP LaSpHUB Large-scale Atomic Simulation with neural network Potential
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WIREs Comput Mol Sci. 2019, e1415 (https://doi.org/10.1002/wcms.1415)
How to get LaSpHUB Large-scale Atomic Simulation with neural network Potential
www.lasphub.com
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How to get LaSpHUB Large-scale Atomic Simulation with neural network Potential
www.lasphub.com
laspmaster@lasphub.com
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How to get LaSpHUB Large-scale Atomic Simulation with neural network Potential
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How to compile LaSpHUB Large-scale Atomic Simulation with neural network Potential
Go to ./Src
make
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How to compile LaSpHUB Large-scale Atomic Simulation with neural network Potential
2. Go to the corresponding
directories, e.g. 1.vasplib
4. Run ./genlib.sh
5. Go to ./Src
make clean
make
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How to compile LaSpHUB Large-scale Atomic Simulation with neural network Potential
Other program
http://www.lasphub.com/tutorial/LASP-lessons.pdf
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How to run LaSpHUB Large-scale Atomic Simulation with neural network Potential
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How to run LaSpHUB Large-scale Atomic Simulation with neural network Potential
Line 6---end:
Element name Cartesian
coordinate x , y z
End lines:
End
End
.arc file is a format utilized by Material Studio
(export as .car)
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How to run LaSpHUB Large-scale Atomic Simulation with neural network Potential
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How to run LaSpHUB Large-scale Atomic Simulation with neural network Potential
lasp.out allkeys.log
Version
Potential type
SSW main
parameters
Results
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Elapse time
How to run LaSpHUB Large-scale Atomic Simulation with neural network Potential
http://www.lasphub.com/Examples.asp LASP_Example
Different purpose
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How to run LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
BFGS
lasp.in
Key words: Explore_type ssw
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Lasp.out (SSW.output=T)
Energy
Stepsize
Order parameter
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Converged energy Symmetry
LaSpHUB Large-scale Atomic Simulation with neural network Potential
SSW
lasp.in
Key words: Explore_type ssw
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Random reaction Continuously add bias potential Remove all the bias
coordinate (mode) and local optimization to potential and optimize to
overcome barriers on the PES find a local minimum.
Monte Carlo is used to
decide the acceptance.
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
SSW.globalcompress 0~1
Compress the configuration
SSW.cell_allowexpand 0~1
Lattice expansion probability
SSW.ds_atom 0.3 ~1
Atomic movement of each gaussian
SSW.NG 6-15
Keywords related to climbing Number of gaussian for atomic movement
behavior of the image
SSW.NG_cell 4-11
Number of gaussian for lattice movement
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
SSW.LowTemp
Allow variable
SSW.HighTemp
temperature set
SSW.TempCycle
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Order parameter
for the initial
and final state in
one SSW
Distance in SSW
Order Parameter
Q2 Q4 and Q6 Maximum force eV/Ang
for new minimum
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Climb Allopt
extrapolation
Most point in SSW trajectories are
close to the minima (red circle) and
lacking of points corresponding to
1. High energy region
2. Extrapolation after adding bias
potential.
Constrained opt
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
(See Example/NNtrain/data-treat)
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
• TrainStr.txt
Structure & energy
• TrainFor.txt
Stress & Force
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
lasp.in
Keywords:
explore_type train
Training set includes
Ntrain 100 100 structures
%block netinfo
the input file of each element
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
“adjust_factor” file:
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
“XXX.input” file:
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
continue:
XXX.input PowerType Structure Descriptors(PTSD)
All the fundamental PTSD paramters,namely S1, S2, S3, S4, S5 and S6
1: H;8: O elements
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
lasp.out:
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Notice:
1. A good NN potential requires bid data. Each point should not
contains too many atoms (<200)
Small data set, such as data from MD can give very high accuracy, but
also very poor generality
DESW
IS FS
Main keywords
Set DESW stepsize
DESW.ds 0.2 Ang For short pathway, reduce DESW.ds
DESW.optpath_cycle 4 Set number of cycles to optimize the pathway
CBD.maxcycle 20 Set number of cycles for CBD method to locate TS
Set converge criterion for TS search
CBD.TSftol 0.1 (maxium atomic force in eV/Ang)
Set converge criterion for TS search
CBD.strftol 0.1 (maxium stress in Gpa)
SSW.output T
SSW.printevery F
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Maximum atomic
$ grep TS lasp.out force component
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Keywords:
SSW.output T
SSW.printevery T
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
SSW.Rotftol_preRot 0.5~1.0
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Searching TS
(energy and force tend to reduce)
Maximum atomic
force at TS
Curvature at TS Energy at TS
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Optimize mode
Cycle-1
Locate the TS
structure
Locate the TS
structure 62
LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
Example6: lasp-external/external-gaussian
Lasp.in
• potential external
the energy is computed using external
program
• External.script lasp.external.sh
the file name of the script, which should be
put in the working directory
(lasp.external.sh by default)
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
When using“external”, the lasp program will give out external.coord, which record
the configuration, as shown in below, in the unit of Å
external.coord
lattice
a(x, y, z)
b(x, y, z)
c(x, y, z)
atom
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
After running the external program, an “external.ene” file should be generated by the
script, which includes energy, atomic force and stress.
As shown below, the unit of energy, force and stress are eV, eV/Å and eV/Å3,
respectively。
external.ene
Energy
stress
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
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How to discuss LaSpHUB Large-scale Atomic Simulation with neural network Potential
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LaSpHUB Large-scale Atomic Simulation with neural network Potential
www.lasphub.com
Thank you!
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