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remove third_order command and ASE based examples to be added in a new pull request

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This commit is contained in:
Axel Kohlmeyer
2019-02-28 15:21:48 -05:00
parent 9298fe7868
commit 7062bc862e
18 changed files with 5 additions and 6532 deletions
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39
examples/USER/phonon/dynamical_matrix_command/GaAs/GaAs.py
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from ase import Atoms, Atom
from ase.calculators.lammpslib import LAMMPSlib
import numpy as np
import matplotlib.pyplot as plt
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
GaAs = Atoms([Atom('Ga', (0.0, 0.0, 0.0)),
Atom('As', (1.413425, 1.413425, 1.413425))],
cell=[(0.0, 2.82685, 2.82685), (2.82685, 0.0, 2.82685), (2.82685, 2.82685, 0.0)],
pbc=True,)
cmds = ["pair_style bop", "pair_coeff * * ../../../../../potentials/GaAs.bop.table Ga As",
"comm_modify cutoff 12"]
mends = ["info system",
"dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
"neigh_modify delay 0"]
N = 5
GaAs = GaAs.repeat([N, N, N])
lammps = LAMMPSlib(lmpcmds=cmds, atom_types={'Ga': 1, 'As': 2}, amendments=mends, log_file='lammps.log')
GaAs.set_calculator(lammps)
GaAs.get_potential_energy()
if rank == 0:
dynmat = np.loadtxt("dynmat.dat")
dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
eigv = np.linalg.eigvals(dynmat)
eigv.sort()
eigv = np.sqrt(np.abs(eigv))/(2*np.pi)
plt.hist(eigv, 80)
plt.xlabel('Frequency (THz)')
plt.show()

39
examples/USER/phonon/dynamical_matrix_command/GaN/GaN.py
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from ase import Atoms, Atom
from ase.calculators.lammpslib import LAMMPSlib
import numpy as np
import matplotlib.pyplot as plt
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
GaN = Atoms([Atom('Ga', (1.59, 0.917986928012, 0.0)),
Atom('Ga', (1.59, -0.917986928012, 2.583)),
Atom('N', (1.59, 0.917986928012, 1.98891)),
Atom('N', (1.59, -0.917986928012, 4.57191))],
cell=[(1.59, -2.75396078403, 0.0), (1.59, 2.75396078403, 0.0), (0.0, 0.0, 5.166)],
pbc=True)
cmds = ["pair_style tersoff", "pair_coeff * * ../../../../../potentials/GaN.tersoff Ga N"]
mends = ["info system",
"dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
"neigh_modify delay 0"]
N = 6
GaN = GaN.repeat([N, N, N])
lammps = LAMMPSlib(lmpcmds=cmds, atom_types={'Ga': 1, 'N': 2}, amendments=mends, log_file='lammps.log')
GaN.set_calculator(lammps)
GaN.get_potential_energy()
if rank == 0:
dynmat = np.loadtxt("dynmat.dat")
dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
eigv = np.linalg.eigvals(dynmat)
eigv.sort()
eigv = np.sqrt(np.abs(eigv))/(2*np.pi)
plt.hist(eigv, 80)
plt.xlabel('Frequency (THz)')
plt.show()

57
examples/USER/phonon/dynamical_matrix_command/Quartz/quartz.py
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@ -1,57 +0,0 @@
from ase import Atoms, Atom
from ase.calculators.lammpslib import LAMMPSlib
import numpy as np
import matplotlib.pyplot as plt
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
quartz = Atoms(
[Atom('Si', (1.1545226, -1.99969180169, 0.0)),
Atom('Si', (1.1545226, 1.99969180169, 3.6036)),
Atom('Si', (2.6069548, 2.15247249027e-16, 1.8018)),
Atom('O', (1.6724232, -0.624132037742, 0.64378314)),
Atom('O', (1.6724232, 0.624132037742, 2.9598186618)),
Atom('O', (2.1623026, -2.49695388906, 4.2473849418)),
Atom('O', (3.5392742, 1.13629495821, 1.1580150582)),
Atom('O', (3.5392742, -1.13629495821, 2.4455813382)),
Atom('O', (2.1623026, 2.49695388906, 4.76161686))],
cell=[(2.458, -4.257380885, 0.0), (2.458, 4.257380885, 0.0), (0.0, 0.0, 5.4054)],
pbc=True,
)
# number of repeats
N = 3
quartz = quartz.repeat([N, N, N])
header = ['units metal',
'atom_style charge',
'atom_modify map array sort 0 0']
cmds = ["pair_style buck/coul/long 10.0 8.0",
"pair_coeff 1 1 0 1 0",
"pair_coeff 1 2 18003.7572 0.20520 133.5381",
"pair_coeff 2 2 1388.7730 0.36232 175.0000",
"kspace_style ewald 1.0e-12",
"set type 1 charge 2.4",
"set type 2 charge -1.2"]
mends = ["dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
"neigh_modify delay 0"]
lammps = LAMMPSlib(lmpcmds=cmds, lammps_header=header, amendments=mends, log_file='lammps.log')
quartz.set_calculator(lammps)
quartz.get_potential_energy()
if rank == 0:
dynmat = np.loadtxt("dynmat.dat")
dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
eigv = np.linalg.eigvals(dynmat)
eigv.sort()
plt.hist(33*np.sqrt(np.abs(eigv))/(2*np.pi), 80)
plt.xlabel('Frequency (cm-1)')
plt.show()

48
examples/USER/phonon/third_order_command/silicon/Manual.md
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# third_order command
## Syntax
```
third_order group-ID style args keyword value ...
```
* group-ID = ID of group of atoms to displace
* style = *regular* or *ballistico*
```
*regular* args = gamma
gamma = finite difference displacement length
*ballistico* args = gamma
gamma = finite difference displacement length
```
* zero or more keyword/value pairs may be appended
* keyword = *file* or *binary*
```
*file* value = output_file
output_file = name of file to dump the dynamical matrix into
*binary* values = *no* or *gzip*
```
## Examples
```
third_order 1 regular 0.000001
third_order 1 ballistico 0.000001
third_order 3 regular 0.00004 file third_order.dat
third_order 5 ballistico 0.00000001 file third_order.dat binary gzip
```
## Description
Calculate the finite difference third order tensor of the selected group.
## Restrictions
None
## Related commands
None
## Default
The option defaults are file = "third_order.dat", binary = no

25
examples/USER/phonon/third_order_command/silicon/README.md
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# LAMMPS LATTICE DYNAMICS COMMANDS
## THIRD ORDER TENSOR CALCULATOR
This directory contains the ingredients to calculate a third order tensor.
Example:
```
$THIRD_ORDER=third_order #tensor output file
NP=4 #number of processors
mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
combine.sh third_order
```
To test out a different silicon example:
```
$THIRD_ORDER=third_order
$LMP_FILE=amorphous_silicon.lmp
cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
NP=4 #number of processors
mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
bash combine.sh $THIRD_ORDER
```
## Requires: MANYBODY and MOLECULE packages

66
examples/USER/phonon/third_order_command/silicon/Si.opt.tersoff
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# Tersoff parameters for various elements and mixtures
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
# other quantities are unitless
# Aidan Thompson (athomps at sandia.gov) takes full blame for this
# file. It specifies various potentials published by J. Tersoff for
# silicon, carbon and germanium. Since Tersoff published several
# different silicon potentials, I refer to them using atom types
# Si(B), Si(C) and Si(D). The last two are almost almost identical but
# refer to two different publications. These names should be used in
# the LAMMPS command when the file is invoked. For example:
# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials
# can be used pure silicon, pure carbon, pure germanium, binary SiC,
# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will
# generate an error if this file is used with any combination
# involving C and Ge, since there are no entries for the GeC
# interactions (Tersoff did not publish parameters for this
# cross-interaction.)
# format of a single entry (one or more lines):
# element 1, element 2, element 3,
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
# The original Tersoff potential for Silicon, Si(B)
# J. Tersoff, PRB, 37, 6991 (1988)
Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7
# The later Tersoff potential for Silicon, Si(C)
# J. Tersoff, PRB, 38, 9902 (1988)
Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734
1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
# The later Tersoff potential for Carbon, Silicon, and Germanium
# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248)
# The Si and C parameters are very close to those in SiC.tersoff
C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6
Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0
C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0
C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0
Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010)
# element 1, element 2, element 3,
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6

17
examples/USER/phonon/third_order_command/silicon/combine.sh
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#!/bin/bash
#This script takes one argument
#The argument is the base name for the split up tensor
#The script then combines and sorts the tensor
#$1 file name
echo "$1"
[ -f $1 ] && rm $1
for i in $(ls ./$1*); do
cat $i >> temp
rm $i
done
sort temp | sort -s -n -k 3 | sort -s -n -k 1 > $1
rm temp

19
examples/USER/phonon/third_order_command/silicon/ff-silicon.lmp
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@ -1,19 +0,0 @@
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Si equal 1
#############
#Atom Masses#
#############
mass ${Si} 28.08550
###########################
#Pair Potentials - Tersoff#
###########################
pair_style tersoff
pair_coeff * * Si.opt.tersoff Si(D)

84
examples/USER/phonon/third_order_command/silicon/in.silicon
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###############################mm
# Atom style - charge/vdw/bonded#
#################################
atom_style full
##############################################
#Units Metal : eV - ps - angstrom - bar#
# Real : kcal/mol - fs - angstrom - atm#
##############################################
units metal
############
#Run number#
############
variable run_no equal 0 # is it a restart?
variable res_no equal ${run_no}-1 # restart file number
#######################################
#Random Seeds and Domain Decomposition#
#######################################
variable iseed0 equal 2357
variable iseed1 equal 26488
variable iseed2 equal 10669
processors * * 1
###########
#Data File#
###########
variable inpfile string silicon_input_file.lmp
variable resfile string final_restart.${res_no}
variable ff_file string ff-silicon.lmp
##########
#Run Type#
##########
variable minimise equal 0 #Energy Minimization
###############################
#Molecular Dynamics Parameters#
###############################
neighbor 1 bin
################################
#Energy Minimization Parameters#
################################
variable mtraj equal 1 # trajectory output frequency - all system
variable etol equal 1e-5 # % change in energy
variable ftol equal 1e-5 # max force threshold (force units)
variable maxiter equal 10000 # max # of iterations
########################
#3D Periodic Simulation#
########################
boundary p p p
#############################
#Reading the input structure#
#############################
if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
#############
#Force Field#
#############
include ${ff_file}
#####################
#Energy Minimization#
#####################
if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
print "Doing CG minimisation"
dump mdcd all dcd ${mtraj} min.dcd
dump_modify mdcd unwrap yes
min_style cg
min_modify line quadratic
minimize ${etol} ${ftol} ${maxiter} ${maxiter}
reset_timestep 0
undump mdcd
label end_minimise
##################
#Dynamical Matrix#
##################
third_order all ballistico 0.00001 file third_order binary no

238
examples/USER/phonon/third_order_command/silicon/lmp_bank/silicon_216.lmp
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@ -1,238 +0,0 @@
LAMMPS description
216 atoms
0 bonds
0 angles
0 dihedrals
0 impropers
1 atom types
0 bond types
0 angle types
0 dihedral types
0 improper types
0.0000000 16.293000 xlo xhi
0.0000000 16.293000 ylo yhi
0.0000000 16.293000 zlo zhi
Atoms
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
2 2 1 0.0000000 0.0000000 2.7160000 2.7160000
3 3 1 0.0000000 2.7160000 2.7160000 0.0000000
4 4 1 0.0000000 2.7160000 0.0000000 2.7160000
5 5 1 0.0000000 4.0730000 1.3580000 4.0730000
6 6 1 0.0000000 1.3580000 1.3580000 1.3580000
7 7 1 0.0000000 1.3580000 4.0730000 4.0730000
8 8 1 0.0000000 4.0730000 4.0730000 1.3580000
9 9 1 0.0000000 0.0000000 0.0000000 5.4310000
10 10 1 0.0000000 0.0000000 2.7160000 8.1460000
11 11 1 0.0000000 2.7160000 2.7160000 5.4310000
12 12 1 0.0000000 2.7160000 0.0000000 8.1460000
13 13 1 0.0000000 4.0730000 1.3580000 9.5040000
14 14 1 0.0000000 1.3580000 1.3580000 6.7890000
15 15 1 0.0000000 1.3580000 4.0730000 9.5040000
16 16 1 0.0000000 4.0730000 4.0730000 6.7890000
17 17 1 0.0000000 0.0000000 0.0000000 10.8620000
18 18 1 0.0000000 0.0000000 2.7160000 13.5780000
19 19 1 0.0000000 2.7160000 2.7160000 10.8620000
20 20 1 0.0000000 2.7160000 0.0000000 13.5780000
21 21 1 0.0000000 4.0730000 1.3580000 14.9350000
22 22 1 0.0000000 1.3580000 1.3580000 12.2200000
23 23 1 0.0000000 1.3580000 4.0730000 14.9350000
24 24 1 0.0000000 4.0730000 4.0730000 12.2200000
25 25 1 0.0000000 0.0000000 5.4310000 0.0000000
26 26 1 0.0000000 0.0000000 8.1460000 2.7160000
27 27 1 0.0000000 2.7160000 8.1460000 0.0000000
28 28 1 0.0000000 2.7160000 5.4310000 2.7160000
29 29 1 0.0000000 4.0730000 6.7890000 4.0730000
30 30 1 0.0000000 1.3580000 6.7890000 1.3580000
31 31 1 0.0000000 1.3580000 9.5040000 4.0730000
32 32 1 0.0000000 4.0730000 9.5040000 1.3580000
33 33 1 0.0000000 0.0000000 5.4310000 5.4310000
34 34 1 0.0000000 0.0000000 8.1460000 8.1460000
35 35 1 0.0000000 2.7160000 8.1460000 5.4310000
36 36 1 0.0000000 2.7160000 5.4310000 8.1460000
37 37 1 0.0000000 4.0730000 6.7890000 9.5040000
38 38 1 0.0000000 1.3580000 6.7890000 6.7890000
39 39 1 0.0000000 1.3580000 9.5040000 9.5040000
40 40 1 0.0000000 4.0730000 9.5040000 6.7890000
41 41 1 0.0000000 0.0000000 5.4310000 10.8620000
42 42 1 0.0000000 0.0000000 8.1460000 13.5780000
43 43 1 0.0000000 2.7160000 8.1460000 10.8620000
44 44 1 0.0000000 2.7160000 5.4310000 13.5780000
45 45 1 0.0000000 4.0730000 6.7890000 14.9350000
46 46 1 0.0000000 1.3580000 6.7890000 12.2200000
47 47 1 0.0000000 1.3580000 9.5040000 14.9350000
48 48 1 0.0000000 4.0730000 9.5040000 12.2200000
49 49 1 0.0000000 0.0000000 10.8620000 0.0000000
50 50 1 0.0000000 0.0000000 13.5780000 2.7160000
51 51 1 0.0000000 2.7160000 13.5780000 0.0000000
52 52 1 0.0000000 2.7160000 10.8620000 2.7160000
53 53 1 0.0000000 4.0730000 12.2200000 4.0730000
54 54 1 0.0000000 1.3580000 12.2200000 1.3580000
55 55 1 0.0000000 1.3580000 14.9350000 4.0730000
56 56 1 0.0000000 4.0730000 14.9350000 1.3580000
57 57 1 0.0000000 0.0000000 10.8620000 5.4310000
58 58 1 0.0000000 0.0000000 13.5780000 8.1460000
59 59 1 0.0000000 2.7160000 13.5780000 5.4310000
60 60 1 0.0000000 2.7160000 10.8620000 8.1460000
61 61 1 0.0000000 4.0730000 12.2200000 9.5040000
62 62 1 0.0000000 1.3580000 12.2200000 6.7890000
63 63 1 0.0000000 1.3580000 14.9350000 9.5040000
64 64 1 0.0000000 4.0730000 14.9350000 6.7890000
65 65 1 0.0000000 0.0000000 10.8620000 10.8620000
66 66 1 0.0000000 0.0000000 13.5780000 13.5780000
67 67 1 0.0000000 2.7160000 13.5780000 10.8620000
68 68 1 0.0000000 2.7160000 10.8620000 13.5780000
69 69 1 0.0000000 4.0730000 12.2200000 14.9350000
70 70 1 0.0000000 1.3580000 12.2200000 12.2200000
71 71 1 0.0000000 1.3580000 14.9350000 14.9350000
72 72 1 0.0000000 4.0730000 14.9350000 12.2200000
73 73 1 0.0000000 5.4310000 0.0000000 0.0000000
74 74 1 0.0000000 5.4310000 2.7160000 2.7160000
75 75 1 0.0000000 8.1460000 2.7160000 0.0000000
76 76 1 0.0000000 8.1460000 0.0000000 2.7160000
77 77 1 0.0000000 9.5040000 1.3580000 4.0730000
78 78 1 0.0000000 6.7890000 1.3580000 1.3580000
79 79 1 0.0000000 6.7890000 4.0730000 4.0730000
80 80 1 0.0000000 9.5040000 4.0730000 1.3580000
81 81 1 0.0000000 5.4310000 0.0000000 5.4310000
82 82 1 0.0000000 5.4310000 2.7160000 8.1460000
83 83 1 0.0000000 8.1460000 2.7160000 5.4310000
84 84 1 0.0000000 8.1460000 0.0000000 8.1460000
85 85 1 0.0000000 9.5040000 1.3580000 9.5040000
86 86 1 0.0000000 6.7890000 1.3580000 6.7890000
87 87 1 0.0000000 6.7890000 4.0730000 9.5040000
88 88 1 0.0000000 9.5040000 4.0730000 6.7890000
89 89 1 0.0000000 5.4310000 0.0000000 10.8620000
90 90 1 0.0000000 5.4310000 2.7160000 13.5780000
91 91 1 0.0000000 8.1460000 2.7160000 10.8620000
92 92 1 0.0000000 8.1460000 0.0000000 13.5780000
93 93 1 0.0000000 9.5040000 1.3580000 14.9350000
94 94 1 0.0000000 6.7890000 1.3580000 12.2200000
95 95 1 0.0000000 6.7890000 4.0730000 14.9350000
96 96 1 0.0000000 9.5040000 4.0730000 12.2200000
97 97 1 0.0000000 5.4310000 5.4310000 0.0000000
98 98 1 0.0000000 5.4310000 8.1460000 2.7160000
99 99 1 0.0000000 8.1460000 8.1460000 0.0000000
100 100 1 0.0000000 8.1460000 5.4310000 2.7160000
101 101 1 0.0000000 9.5040000 6.7890000 4.0730000
102 102 1 0.0000000 6.7890000 6.7890000 1.3580000
103 103 1 0.0000000 6.7890000 9.5040000 4.0730000
104 104 1 0.0000000 9.5040000 9.5040000 1.3580000
105 105 1 0.0000000 5.4310000 5.4310000 5.4310000
106 106 1 0.0000000 5.4310000 8.1460000 8.1460000
107 107 1 0.0000000 8.1460000 8.1460000 5.4310000
108 108 1 0.0000000 8.1460000 5.4310000 8.1460000
109 109 1 0.0000000 9.5040000 6.7890000 9.5040000
110 110 1 0.0000000 6.7890000 6.7890000 6.7890000
111 111 1 0.0000000 6.7890000 9.5040000 9.5040000
112 112 1 0.0000000 9.5040000 9.5040000 6.7890000
113 113 1 0.0000000 5.4310000 5.4310000 10.8620000
114 114 1 0.0000000 5.4310000 8.1460000 13.5780000
115 115 1 0.0000000 8.1460000 8.1460000 10.8620000
116 116 1 0.0000000 8.1460000 5.4310000 13.5780000
117 117 1 0.0000000 9.5040000 6.7890000 14.9350000
118 118 1 0.0000000 6.7890000 6.7890000 12.2200000
119 119 1 0.0000000 6.7890000 9.5040000 14.9350000
120 120 1 0.0000000 9.5040000 9.5040000 12.2200000
121 121 1 0.0000000 5.4310000 10.8620000 0.0000000
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534
examples/USER/phonon/third_order_command/silicon/lmp_bank/silicon_512.lmp
View File

@ -1,534 +0,0 @@
LAMMPS description
512 atoms
0 bonds
0 angles
0 dihedrals
0 impropers
1 atom types
0 bond types
0 angle types
0 dihedral types
0 improper types
0.0000000 21.724000 xlo xhi
0.0000000 21.724000 ylo yhi
0.0000000 21.724000 zlo zhi
Atoms
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299 299 1 0.0000000 13.5770000 8.1460000 5.4310000
300 300 1 0.0000000 13.5770000 5.4310000 8.1460000
301 301 1 0.0000000 14.9350000 6.7890000 9.5040000
302 302 1 0.0000000 12.2200000 6.7890000 6.7890000
303 303 1 0.0000000 12.2200000 9.5040000 9.5040000
304 304 1 0.0000000 14.9350000 9.5040000 6.7890000
305 305 1 0.0000000 10.8620000 5.4310000 10.8620000
306 306 1 0.0000000 10.8620000 8.1460000 13.5770000
307 307 1 0.0000000 13.5770000 8.1460000 10.8620000
308 308 1 0.0000000 13.5770000 5.4310000 13.5770000
309 309 1 0.0000000 14.9350000 6.7890000 14.9350000
310 310 1 0.0000000 12.2200000 6.7890000 12.2200000
311 311 1 0.0000000 12.2200000 9.5040000 14.9350000
312 312 1 0.0000000 14.9350000 9.5040000 12.2200000
313 313 1 0.0000000 10.8620000 5.4310000 16.2930000
314 314 1 0.0000000 10.8620000 8.1460000 19.0080000
315 315 1 0.0000000 13.5770000 8.1460000 16.2930000
316 316 1 0.0000000 13.5770000 5.4310000 19.0080000
317 317 1 0.0000000 14.9350000 6.7890000 20.3660000
318 318 1 0.0000000 12.2200000 6.7890000 17.6510000
319 319 1 0.0000000 12.2200000 9.5040000 20.3660000
320 320 1 0.0000000 14.9350000 9.5040000 17.6510000
321 321 1 0.0000000 10.8620000 10.8620000 0.0000000
322 322 1 0.0000000 10.8620000 13.5770000 2.7150000
323 323 1 0.0000000 13.5770000 13.5770000 0.0000000
324 324 1 0.0000000 13.5770000 10.8620000 2.7150000
325 325 1 0.0000000 14.9350000 12.2200000 4.0730000
326 326 1 0.0000000 12.2200000 12.2200000 1.3580000
327 327 1 0.0000000 12.2200000 14.9350000 4.0730000
328 328 1 0.0000000 14.9350000 14.9350000 1.3580000
329 329 1 0.0000000 10.8620000 10.8620000 5.4310000
330 330 1 0.0000000 10.8620000 13.5770000 8.1460000
331 331 1 0.0000000 13.5770000 13.5770000 5.4310000
332 332 1 0.0000000 13.5770000 10.8620000 8.1460000
333 333 1 0.0000000 14.9350000 12.2200000 9.5040000
334 334 1 0.0000000 12.2200000 12.2200000 6.7890000
335 335 1 0.0000000 12.2200000 14.9350000 9.5040000
336 336 1 0.0000000 14.9350000 14.9350000 6.7890000
337 337 1 0.0000000 10.8620000 10.8620000 10.8620000
338 338 1 0.0000000 10.8620000 13.5770000 13.5770000
339 339 1 0.0000000 13.5770000 13.5770000 10.8620000
340 340 1 0.0000000 13.5770000 10.8620000 13.5770000
341 341 1 0.0000000 14.9350000 12.2200000 14.9350000
342 342 1 0.0000000 12.2200000 12.2200000 12.2200000
343 343 1 0.0000000 12.2200000 14.9350000 14.9350000
344 344 1 0.0000000 14.9350000 14.9350000 12.2200000
345 345 1 0.0000000 10.8620000 10.8620000 16.2930000
346 346 1 0.0000000 10.8620000 13.5770000 19.0080000
347 347 1 0.0000000 13.5770000 13.5770000 16.2930000
348 348 1 0.0000000 13.5770000 10.8620000 19.0080000
349 349 1 0.0000000 14.9350000 12.2200000 20.3660000
350 350 1 0.0000000 12.2200000 12.2200000 17.6510000
351 351 1 0.0000000 12.2200000 14.9350000 20.3660000
352 352 1 0.0000000 14.9350000 14.9350000 17.6510000
353 353 1 0.0000000 10.8620000 16.2930000 0.0000000
354 354 1 0.0000000 10.8620000 19.0080000 2.7150000
355 355 1 0.0000000 13.5770000 19.0080000 0.0000000
356 356 1 0.0000000 13.5770000 16.2930000 2.7150000
357 357 1 0.0000000 14.9350000 17.6510000 4.0730000
358 358 1 0.0000000 12.2200000 17.6510000 1.3580000
359 359 1 0.0000000 12.2200000 20.3660000 4.0730000
360 360 1 0.0000000 14.9350000 20.3660000 1.3580000
361 361 1 0.0000000 10.8620000 16.2930000 5.4310000
362 362 1 0.0000000 10.8620000 19.0080000 8.1460000
363 363 1 0.0000000 13.5770000 19.0080000 5.4310000
364 364 1 0.0000000 13.5770000 16.2930000 8.1460000
365 365 1 0.0000000 14.9350000 17.6510000 9.5040000
366 366 1 0.0000000 12.2200000 17.6510000 6.7890000
367 367 1 0.0000000 12.2200000 20.3660000 9.5040000
368 368 1 0.0000000 14.9350000 20.3660000 6.7890000
369 369 1 0.0000000 10.8620000 16.2930000 10.8620000
370 370 1 0.0000000 10.8620000 19.0080000 13.5770000
371 371 1 0.0000000 13.5770000 19.0080000 10.8620000
372 372 1 0.0000000 13.5770000 16.2930000 13.5770000
373 373 1 0.0000000 14.9350000 17.6510000 14.9350000
374 374 1 0.0000000 12.2200000 17.6510000 12.2200000
375 375 1 0.0000000 12.2200000 20.3660000 14.9350000
376 376 1 0.0000000 14.9350000 20.3660000 12.2200000
377 377 1 0.0000000 10.8620000 16.2930000 16.2930000
378 378 1 0.0000000 10.8620000 19.0080000 19.0080000
379 379 1 0.0000000 13.5770000 19.0080000 16.2930000
380 380 1 0.0000000 13.5770000 16.2930000 19.0080000
381 381 1 0.0000000 14.9350000 17.6510000 20.3660000
382 382 1 0.0000000 12.2200000 17.6510000 17.6510000
383 383 1 0.0000000 12.2200000 20.3660000 20.3660000
384 384 1 0.0000000 14.9350000 20.3660000 17.6510000
385 385 1 0.0000000 16.2930000 0.0000000 0.0000000
386 386 1 0.0000000 16.2930000 2.7150000 2.7150000
387 387 1 0.0000000 19.0080000 2.7150000 0.0000000
388 388 1 0.0000000 19.0080000 0.0000000 2.7150000
389 389 1 0.0000000 20.3660000 1.3580000 4.0730000
390 390 1 0.0000000 17.6510000 1.3580000 1.3580000
391 391 1 0.0000000 17.6510000 4.0730000 4.0730000
392 392 1 0.0000000 20.3660000 4.0730000 1.3580000
393 393 1 0.0000000 16.2930000 0.0000000 5.4310000
394 394 1 0.0000000 16.2930000 2.7150000 8.1460000
395 395 1 0.0000000 19.0080000 2.7150000 5.4310000
396 396 1 0.0000000 19.0080000 0.0000000 8.1460000
397 397 1 0.0000000 20.3660000 1.3580000 9.5040000
398 398 1 0.0000000 17.6510000 1.3580000 6.7890000
399 399 1 0.0000000 17.6510000 4.0730000 9.5040000
400 400 1 0.0000000 20.3660000 4.0730000 6.7890000
401 401 1 0.0000000 16.2930000 0.0000000 10.8620000
402 402 1 0.0000000 16.2930000 2.7150000 13.5770000
403 403 1 0.0000000 19.0080000 2.7150000 10.8620000
404 404 1 0.0000000 19.0080000 0.0000000 13.5770000
405 405 1 0.0000000 20.3660000 1.3580000 14.9350000
406 406 1 0.0000000 17.6510000 1.3580000 12.2200000
407 407 1 0.0000000 17.6510000 4.0730000 14.9350000
408 408 1 0.0000000 20.3660000 4.0730000 12.2200000
409 409 1 0.0000000 16.2930000 0.0000000 16.2930000
410 410 1 0.0000000 16.2930000 2.7150000 19.0080000
411 411 1 0.0000000 19.0080000 2.7150000 16.2930000
412 412 1 0.0000000 19.0080000 0.0000000 19.0080000
413 413 1 0.0000000 20.3660000 1.3580000 20.3660000
414 414 1 0.0000000 17.6510000 1.3580000 17.6510000
415 415 1 0.0000000 17.6510000 4.0730000 20.3660000
416 416 1 0.0000000 20.3660000 4.0730000 17.6510000
417 417 1 0.0000000 16.2930000 5.4310000 0.0000000
418 418 1 0.0000000 16.2930000 8.1460000 2.7150000
419 419 1 0.0000000 19.0080000 8.1460000 0.0000000
420 420 1 0.0000000 19.0080000 5.4310000 2.7150000
421 421 1 0.0000000 20.3660000 6.7890000 4.0730000
422 422 1 0.0000000 17.6510000 6.7890000 1.3580000
423 423 1 0.0000000 17.6510000 9.5040000 4.0730000
424 424 1 0.0000000 20.3660000 9.5040000 1.3580000
425 425 1 0.0000000 16.2930000 5.4310000 5.4310000
426 426 1 0.0000000 16.2930000 8.1460000 8.1460000
427 427 1 0.0000000 19.0080000 8.1460000 5.4310000
428 428 1 0.0000000 19.0080000 5.4310000 8.1460000
429 429 1 0.0000000 20.3660000 6.7890000 9.5040000
430 430 1 0.0000000 17.6510000 6.7890000 6.7890000
431 431 1 0.0000000 17.6510000 9.5040000 9.5040000
432 432 1 0.0000000 20.3660000 9.5040000 6.7890000
433 433 1 0.0000000 16.2930000 5.4310000 10.8620000
434 434 1 0.0000000 16.2930000 8.1460000 13.5770000
435 435 1 0.0000000 19.0080000 8.1460000 10.8620000
436 436 1 0.0000000 19.0080000 5.4310000 13.5770000
437 437 1 0.0000000 20.3660000 6.7890000 14.9350000
438 438 1 0.0000000 17.6510000 6.7890000 12.2200000
439 439 1 0.0000000 17.6510000 9.5040000 14.9350000
440 440 1 0.0000000 20.3660000 9.5040000 12.2200000
441 441 1 0.0000000 16.2930000 5.4310000 16.2930000
442 442 1 0.0000000 16.2930000 8.1460000 19.0080000
443 443 1 0.0000000 19.0080000 8.1460000 16.2930000
444 444 1 0.0000000 19.0080000 5.4310000 19.0080000
445 445 1 0.0000000 20.3660000 6.7890000 20.3660000
446 446 1 0.0000000 17.6510000 6.7890000 17.6510000
447 447 1 0.0000000 17.6510000 9.5040000 20.3660000
448 448 1 0.0000000 20.3660000 9.5040000 17.6510000
449 449 1 0.0000000 16.2930000 10.8620000 0.0000000
450 450 1 0.0000000 16.2930000 13.5770000 2.7150000
451 451 1 0.0000000 19.0080000 13.5770000 0.0000000
452 452 1 0.0000000 19.0080000 10.8620000 2.7150000
453 453 1 0.0000000 20.3660000 12.2200000 4.0730000
454 454 1 0.0000000 17.6510000 12.2200000 1.3580000
455 455 1 0.0000000 17.6510000 14.9350000 4.0730000
456 456 1 0.0000000 20.3660000 14.9350000 1.3580000
457 457 1 0.0000000 16.2930000 10.8620000 5.4310000
458 458 1 0.0000000 16.2930000 13.5770000 8.1460000
459 459 1 0.0000000 19.0080000 13.5770000 5.4310000
460 460 1 0.0000000 19.0080000 10.8620000 8.1460000
461 461 1 0.0000000 20.3660000 12.2200000 9.5040000
462 462 1 0.0000000 17.6510000 12.2200000 6.7890000
463 463 1 0.0000000 17.6510000 14.9350000 9.5040000
464 464 1 0.0000000 20.3660000 14.9350000 6.7890000
465 465 1 0.0000000 16.2930000 10.8620000 10.8620000
466 466 1 0.0000000 16.2930000 13.5770000 13.5770000
467 467 1 0.0000000 19.0080000 13.5770000 10.8620000
468 468 1 0.0000000 19.0080000 10.8620000 13.5770000
469 469 1 0.0000000 20.3660000 12.2200000 14.9350000
470 470 1 0.0000000 17.6510000 12.2200000 12.2200000
471 471 1 0.0000000 17.6510000 14.9350000 14.9350000
472 472 1 0.0000000 20.3660000 14.9350000 12.2200000
473 473 1 0.0000000 16.2930000 10.8620000 16.2930000
474 474 1 0.0000000 16.2930000 13.5770000 19.0080000
475 475 1 0.0000000 19.0080000 13.5770000 16.2930000
476 476 1 0.0000000 19.0080000 10.8620000 19.0080000
477 477 1 0.0000000 20.3660000 12.2200000 20.3660000
478 478 1 0.0000000 17.6510000 12.2200000 17.6510000
479 479 1 0.0000000 17.6510000 14.9350000 20.3660000
480 480 1 0.0000000 20.3660000 14.9350000 17.6510000
481 481 1 0.0000000 16.2930000 16.2930000 0.0000000
482 482 1 0.0000000 16.2930000 19.0080000 2.7150000
483 483 1 0.0000000 19.0080000 19.0080000 0.0000000
484 484 1 0.0000000 19.0080000 16.2930000 2.7150000
485 485 1 0.0000000 20.3660000 17.6510000 4.0730000
486 486 1 0.0000000 17.6510000 17.6510000 1.3580000
487 487 1 0.0000000 17.6510000 20.3660000 4.0730000
488 488 1 0.0000000 20.3660000 20.3660000 1.3580000
489 489 1 0.0000000 16.2930000 16.2930000 5.4310000
490 490 1 0.0000000 16.2930000 19.0080000 8.1460000
491 491 1 0.0000000 19.0080000 19.0080000 5.4310000
492 492 1 0.0000000 19.0080000 16.2930000 8.1460000
493 493 1 0.0000000 20.3660000 17.6510000 9.5040000
494 494 1 0.0000000 17.6510000 17.6510000 6.7890000
495 495 1 0.0000000 17.6510000 20.3660000 9.5040000
496 496 1 0.0000000 20.3660000 20.3660000 6.7890000
497 497 1 0.0000000 16.2930000 16.2930000 10.8620000
498 498 1 0.0000000 16.2930000 19.0080000 13.5770000
499 499 1 0.0000000 19.0080000 19.0080000 10.8620000
500 500 1 0.0000000 19.0080000 16.2930000 13.5770000
501 501 1 0.0000000 20.3660000 17.6510000 14.9350000
502 502 1 0.0000000 17.6510000 17.6510000 12.2200000
503 503 1 0.0000000 17.6510000 20.3660000 14.9350000
504 504 1 0.0000000 20.3660000 20.3660000 12.2200000
505 505 1 0.0000000 16.2930000 16.2930000 16.2930000
506 506 1 0.0000000 16.2930000 19.0080000 19.0080000
507 507 1 0.0000000 19.0080000 19.0080000 16.2930000
508 508 1 0.0000000 19.0080000 16.2930000 19.0080000
509 509 1 0.0000000 20.3660000 17.6510000 20.3660000
510 510 1 0.0000000 17.6510000 17.6510000 17.6510000
511 511 1 0.0000000 17.6510000 20.3660000 20.3660000
512 512 1 0.0000000 20.3660000 20.3660000 17.6510000

29
examples/USER/phonon/third_order_command/silicon/lmp_bank/silicon_8.lmp
View File

@ -1,29 +0,0 @@
LAMMPS description
8 atoms
0 bonds
0 angles
0 dihedrals
0 impropers
1 atom types
0 bond types
0 angle types
0 dihedral types
0 improper types
0.0000000 5.4310000 xlo xhi
0.0000000 5.4310000 ylo yhi
0.0000000 5.4310000 zlo zhi
Atoms
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500

58
examples/USER/phonon/third_order_command/silicon/results/out.silicon
View File

@ -1,58 +0,0 @@
LAMMPS (16 Jul 2018)
Reading data file ...
orthogonal box = (0 0 0) to (5.431 5.431 5.431)
2 by 2 by 1 MPI processor grid
reading atoms ...
8 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4
ghost atom cutoff = 4
binsize = 2, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Calculating Anharmonic Dynamical Matrix...
Third Order calculation took 0.043923 seconds
Finished Calculating Third Order Tensor
Loop time of 1.22619e+06 on 4 procs for 0 steps with 8 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013707 | 0.016582 | 0.019588 | 2.2 | 0.00
Bond | 8.1341e-05 | 8.7207e-05 | 9.3228e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019285 | 0.022435 | 0.025684 | 2.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.226e+06 | | |100.00
Nlocal: 2 ave 2 max 2 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 56 ave 56 max 56 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 128
Ave neighs/atom = 16
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

4608
examples/USER/phonon/third_order_command/silicon/results/third_order
View File

File diff suppressed because it is too large Load Diff

29
examples/USER/phonon/third_order_command/silicon/silicon_input_file.lmp
View File

@ -1,29 +0,0 @@
LAMMPS description
8 atoms
0 bonds
0 angles
0 dihedrals
0 impropers
1 atom types
0 bond types
0 angle types
0 dihedral types
0 improper types
0.0000000 5.4310000 xlo xhi
0.0000000 5.4310000 ylo yhi
0.0000000 5.4310000 zlo zhi
Atoms
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500

11
src/USER-PHONON/README
View File

@ -3,12 +3,11 @@ matrices from finite temperature MD simulations, which can then be
used to compute phonon dispersion relations, directly from molecular
dynamics simulations.
It also contains two commands to compute the dynamical matrix and
the corresponding third order matrix at pre-optimized positions
through finite differences.
It also contains a command to compute the dynamical matrix at
pre-optimized positions through finite differences.
See the doc page for the fix phonon command or the dynamical_matrix
third_order commands for detailed usage instructions.
command for detailed usage instructions.
Use of this package requires building LAMMPS with FFT suppport, as
described in doc/Section_start.html.
@ -30,5 +29,5 @@ The person who created fix phonon is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.
The person who created dynamical_matrix and third_order is
Charlie Sievers at UC Davis.
The person who created the dynamical_matrix command is Charlie Sievers
at UC Davis. Contact him directly if you have questions about his code.

560
src/USER-PHONON/third_order.cpp
View File

@ -1,560 +0,0 @@
//
// Created by charlie sievers on 7/5/18.
//
#include <mpi.h>
#include <cstdlib>
#include "third_order.h"
#include "atom.h"
#include "complex"
#include "domain.h"
#include "comm.h"
#include "group.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "update.h"
#include "neighbor.h"
#include "pair.h"
#include "timer.h"
#include "finish.h"
#include <algorithm>
using namespace LAMMPS_NS;
enum{REGULAR,BALLISTICO};
/* ---------------------------------------------------------------------- */
ThirdOrder::ThirdOrder(LAMMPS *lmp) : Pointers(lmp), fp(NULL)
{
external_force_clear = 1;
}
/* ---------------------------------------------------------------------- */
ThirdOrder::~ThirdOrder()
{
if (fp && me == 0) fclose(fp);
memory->destroy(groupmap);
fp = NULL;
}
/* ----------------------------------------------------------------------
setup without output or one-time post-init setup
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void ThirdOrder::setup()
{
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->image_check();
domain->box_too_small_check();
neighbor->build(1);
neighbor->ncalls = 0;
neighbor->every = 3; // build every this many steps
neighbor->delay = 1;
neighbor->ago = 0;
neighbor->ndanger = 0;
// compute all forces
external_force_clear = 0;
eflag=0;
vflag=0;
update_force();
if (gcount == atom->natoms)
for (bigint i=0; i<atom->natoms; i++)
groupmap[i] = i;
else
create_groupmap();
}
/* ---------------------------------------------------------------------- */
void ThirdOrder::command(int narg, char **arg)
{
MPI_Comm_rank(world,&me);
if (domain->box_exist == 0)
error->all(FLERR,"Third_order command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal third_oreder command");
lmp->init();
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
else pair_compute_flag = 0;
if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
else kspace_compute_flag = 0;
// group and style
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find third_order group ID");
groupbit = group->bitmask[igroup];
gcount = group->count(igroup);
dynlen = (gcount)*3;
memory->create(groupmap,atom->natoms,"total_group_map:totalgm");
update->setupflag = 1;
int style = -1;
if (strcmp(arg[1],"regular") == 0) style = REGULAR;
else if (strcmp(arg[1],"ballistico") == 0) style = BALLISTICO;
else error->all(FLERR,"Illegal Dynamical Matrix command");
// set option defaults
binaryflag = 0;
scaleflag = 0;
compressed = 0;
file_flag = 0;
file_opened = 0;
conversion = 1;
// read options from end of input line
if (style == REGULAR) options(narg-3,&arg[3]); //COME BACK
else if (style == BALLISTICO) options(narg-3,&arg[3]); //COME BACK
else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n");
del = force->numeric(FLERR, arg[2]);
// move atoms by 3-vector or specified variable(s)
if (style == REGULAR) {
setup();
timer->init();
timer->barrier_start();
calculateMatrix();
timer->barrier_stop();
}
if (style == BALLISTICO) {
setup();
convert_units(update->unit_style);
conversion = conv_energy/conv_distance/conv_distance;
timer->init();
timer->barrier_start();
calculateMatrix();
timer->barrier_stop();
}
Finish finish(lmp);
finish.end(1);
}
/* ----------------------------------------------------------------------
parse optional parameters
------------------------------------------------------------------------- */
void ThirdOrder::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal dynamical_matrix command");
int iarg = 0;
const char *filename = "third_order.txt";
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR, "Illegal dynamical_matrix command");
filename = arg[iarg + 1];
file_flag = 1;
iarg += 2;
}
else if (strcmp(arg[iarg],"binary") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal dynamical_matrix command");
if (strcmp(arg[iarg+1],"gzip") == 0) {
compressed = 1;
}
else if (strcmp(arg[iarg+1],"yes") == 0) {
binaryflag = 1;
}
iarg += 2;
} else error->all(FLERR,"Illegal dynamical_matrix command");
}
if (file_flag == 1 && me == 0) {
openfile(filename);
}
}
/* ----------------------------------------------------------------------
generic opening of a file
ASCII or binary or gzipped
some derived classes override this function
------------------------------------------------------------------------- */
void ThirdOrder::openfile(const char* filename)
{
// if file already opened, return
if (file_opened) return;
if (compressed) {
#ifdef LAMMPS_GZIP
char gzip[128];
sprintf(gzip,"gzip -6 > %s",filename);
#ifdef _WIN32
fp = _popen(gzip,"wb");
#else
fp = popen(gzip,"w");
#endif
#else
error->one(FLERR,"Cannot open gzipped file");
#endif
} else if (binaryflag) {
fp = fopen(filename,"wb");
} else {
fp = fopen(filename,"w");
}
if (fp == NULL) error->one(FLERR,"Cannot open dump file");
file_opened = 1;
}
/* ----------------------------------------------------------------------
create dynamical matrix
------------------------------------------------------------------------- */
void ThirdOrder::calculateMatrix()
{
int local_idx; // local index
int local_jdx; // second local index
int local_kdx; // third local index
int nlocal = atom->nlocal;
int natoms = atom->natoms;
int *gm = groupmap;
double **f = atom->f;
double *dynmat = new double[3*dynlen];
double *fdynmat = new double[3*dynlen];
memset(&dynmat[0],0,dynlen*sizeof(double));
memset(&fdynmat[0],0,dynlen*sizeof(double));
if (comm->me == 0 && screen) fprintf(screen,"Calculating Anharmonic Dynamical Matrix...\n");
update->nsteps = 0;
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
for (bigint alpha=0; alpha<3; alpha++){
for (bigint j=1; j<=natoms; j++){
local_jdx = atom->map(j);
for (int beta=0; beta<3; beta++){
displace_atom(local_idx, alpha, 1);
displace_atom(local_jdx, beta, 1);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
}
}
}
displace_atom(local_jdx, beta, -2);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
}
}
}
displace_atom(local_jdx, beta, 1);
displace_atom(local_idx,alpha,-2);
displace_atom(local_jdx, beta, 1);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
}
}
}
displace_atom(local_jdx, beta, -2);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
dynmat[gm[k-1]*3+gamma] /= -(4 * del * del);
}
}
}
displace_atom(local_jdx, beta, 1);
displace_atom(local_idx, alpha, 1);
MPI_Reduce(dynmat,fdynmat,3*dynlen,MPI_DOUBLE,MPI_SUM,0,world);
if (me == 0){
writeMatrix(fdynmat, gm[i-1], alpha, gm[j-1], beta);
}
memset(&dynmat[0],0,dynlen*sizeof(double));
}
}
}
}
delete [] dynmat;
delete [] fdynmat;
if (screen && me ==0 ) fprintf(screen,"Finished Calculating Third Order Tensor\n");
}
/* ----------------------------------------------------------------------
write dynamical matrix
------------------------------------------------------------------------- */
void ThirdOrder::writeMatrix(double *dynmat, int i, int a, int j, int b)
{
if (me != 0)
return;
if (!binaryflag && fp) {
clearerr(fp);
for (int k = 0; k < gcount; k++){
if (dynmat[k*3] > 1.0e-16
&& dynmat[k*3+1] > 1.0e-16
&& dynmat[k*3+2] > 1.0e-16)
fprintf(fp,
"%d %d %d %d %d %7.8f %7.8f %7.8f\n",
i+1, a + 1, j+1, b + 1, groupmap[k]+1,
dynmat[k*3] * conversion,
dynmat[k*3+1] * conversion,
dynmat[k*3+2] * conversion);
}
}
else if (binaryflag && fp){
clearerr(fp);
fwrite(&dynmat[0], sizeof(double), dynlen, fp);
}
if (ferror(fp)) error->one(FLERR,"Error writing to file");
}
/* ----------------------------------------------------------------------
Displace atoms
---------------------------------------------------------------------- */
void ThirdOrder::displace_atom(int local_idx, int direction, int magnitude)
{
if (local_idx < 0) return;
double **x = atom->x;
int *sametag = atom->sametag;
int j = local_idx;
x[local_idx][direction] += del*magnitude;
while (sametag[j] >= 0){
j = sametag[j];
x[j][direction] += del*magnitude;
}
}
/* ----------------------------------------------------------------------
evaluate potential energy and forces
may migrate atoms due to reneighboring
return new energy, which should include nextra_global dof
return negative gradient stored in atom->f
return negative gradient for nextra_global dof in fextra
------------------------------------------------------------------------- */
void ThirdOrder::update_force()
{
force_clear();
timer->stamp();
if (pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
if (force->newton) {
comm->reverse_comm();
timer->stamp(Timer::COMM);
}
++ update->nsteps;
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
clear other arrays as needed
------------------------------------------------------------------------- */
void ThirdOrder::force_clear()
{
if (external_force_clear) return;
// clear global force array
// if either newton flag is set, also include ghosts
size_t nbytes = sizeof(double) * atom->nlocal;
if (force->newton) nbytes += sizeof(double) * atom->nghost;
if (nbytes) {
memset(&atom->f[0][0],0,3*nbytes);
}
}
/* ---------------------------------------------------------------------- */
void ThirdOrder::convert_units(const char *style)
{
// physical constants from:
// http://physics.nist.gov/cuu/Constants/Table/allascii.txt
// using thermochemical calorie = 4.184 J
if (strcmp(style,"lj") == 0) {
error->all(FLERR,"Conversion Not Set");
//conversion = 1; // lj -> 10 J/mol
} else if (strcmp(style,"real") == 0) {
conv_energy = 418.4; // kcal/mol -> 10 J/mol
conv_mass = 1; // g/mol -> g/mol
conv_distance = 1; // angstrom -> angstrom
} else if (strcmp(style,"metal") == 0) {
conv_energy = 9648.5; // eV -> 10 J/mol
conv_mass = 1; // g/mol -> g/mol
conv_distance = 1; // angstrom -> angstrom
} else if (strcmp(style,"si") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
conv_energy = 6.022E22; // J -> 10 J/mol
conv_mass = 6.022E26; // kg -> g/mol
conv_distance = 1E-10; // meter -> angstrom
} else if (strcmp(style,"cgs") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
conv_energy = 6.022E12; // Erg -> 10 J/mol
conv_mass = 6.022E23; // g -> g/mol
conv_distance = 1E-7; // centimeter -> angstrom
} else if (strcmp(style,"electron") == 0) {
conv_energy = 262550; // Hartree -> 10 J/mol
conv_mass = 1; // amu -> g/mol
conv_distance = 0.529177249; // bohr -> angstrom
} else if (strcmp(style,"micro") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
conv_energy = 6.022E10; // picogram-micrometer^2/microsecond^2 -> 10 J/mol
conv_mass = 6.022E11; // pg -> g/mol
conv_distance = 1E-4; // micrometer -> angstrom
} else if (strcmp(style,"nano") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
conv_energy = 6.022E4; // attogram-nanometer^2/nanosecond^2 -> 10 J/mol
conv_mass = 6.022E5; // ag -> g/mol
conv_distance = 0.1; // angstrom -> angstrom
} else error->all(FLERR,"Units Type Conversion Not Found");
}
/* ---------------------------------------------------------------------- */
void ThirdOrder::create_groupmap()
{
//Create a group map which maps atom order onto group
int local_idx; // local index
int gid = 0; //group index
int nlocal = atom->nlocal;
int *mask = atom->mask;
bigint natoms = atom->natoms;
int *recv = new int[comm->nprocs];
int *displs = new int[comm->nprocs];
int *temp_groupmap = new int[natoms];
//find number of local atoms in the group (final_gid)
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
gid += 1; // gid at the end of loop is final_Gid
}
//create an array of length final_gid
int *sub_groupmap = new int[gid];
gid = 0;
//create a map between global atom id and group atom id for each proc
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit){
sub_groupmap[gid] = i;
gid += 1;
}
}
//populate arrays for Allgatherv
for (int i=0; i<comm->nprocs; i++){
recv[i] = 0;
}
recv[comm->me] = gid;
MPI_Allreduce(recv,displs,4,MPI_INT,MPI_SUM,world);
for (int i=0; i<comm->nprocs; i++){
recv[i]=displs[i];
if (i>0) displs[i] = displs[i-1]+recv[i-1];
else displs[i] = 0;
}
//combine subgroup maps into total temporary groupmap
MPI_Allgatherv(sub_groupmap,gid,MPI_INT,temp_groupmap,recv,displs,MPI_INT,world);
std::sort(temp_groupmap,temp_groupmap+gcount);
//populate member groupmap based on temp groupmap
for (bigint i=0; i<natoms; i++){
if (i==temp_groupmap[i]-1)
groupmap[i] = temp_groupmap[i]-1;
else
groupmap[i] = -1;
}
//free that memory!
delete[] recv;
delete[] displs;
delete[] sub_groupmap;
delete[] temp_groupmap;
}

76
src/USER-PHONON/third_order.h
View File

@ -1,76 +0,0 @@
//
// Created by charlie sievers on 7/5/18.
//
#ifdef COMMAND_CLASS
CommandStyle(third_order,ThirdOrder)
#else
#ifndef LMP_THIRD_ORDER_H
#define LMP_THIRD_ORDER_H
#include "pointers.h"
namespace LAMMPS_NS {
class ThirdOrder : protected Pointers {
public:
ThirdOrder(class LAMMPS *);
virtual ~ThirdOrder();
void command(int, char **);
void setup();
protected:
int eflag,vflag; // flags for energy/virial computation
int external_force_clear; // clear forces locally or externally
int triclinic; // 0 if domain is orthog, 1 if triclinic
int pairflag;
int pair_compute_flag; // 0 if pair->compute is skipped
int kspace_compute_flag; // 0 if kspace->compute is skipped
int nvec; // local atomic dof = length of xvec
void update_force();
void force_clear();
virtual void openfile(const char* filename);
private:
void options(int, char **);
void create_groupmap();
void calculateMatrix();
void convert_units(const char *style);
void displace_atom(int local_idx, int direction, int magnitude);
void writeMatrix(double *, int, int, int, int);
double conversion;
double conv_energy;
double conv_distance;
double conv_mass;
double del;
int igroup,groupbit;
bigint dynlen;
int scaleflag;
int me;
int gcount; // number of atoms in group
int *groupmap;
int compressed; // 1 if dump file is written compressed, 0 no
int binaryflag; // 1 if dump file is written binary, 0 no
int file_opened; // 1 if openfile method has been called, 0 no
int file_flag; // 1 custom file name, 0 dynmat.dat
FILE *fp;
};
}
#endif //LMP_THIRD_ORDER_H
#endif