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39
examples/USER/phonon/1-1D-mono/README Normal file
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This directory illustrates the usage of fix-phonon to calculate the dynamical
matrix as well as phonon dispersion curve for 1 dimensional monoatomic chain.
The files under this directory:
1) data.pos : LAMMPS input file
2) disp.dat : phonon dispersion data from phonon.bin.1500000
3) in.Ana : LAMMPS input file
4) in.disp : input file to get disp.dat by phana
5) log.lammps : LAMMPS log file
6) map.in : LAMMPS input file for fix-phonon
7) pdisp.eps : phonon dispersion for 1D monoatomic chain, generated by plot.disp
8) phonon.bin.2000000 : last output binary file by fix-phonon
9) phonon.log : log file for fix-phonon
10) plot.disp : script to generate phonon dispersion curve (old)
11) README : this file
To run this example, simply:
-> lmp -in in.Ana -screen none
Once done, one can use the auxiliary analysing code "phana" to obtain "disp.dat" based on
data from phonon.bin.2000000:
-> phana phonon.bin.2000000 < in.disp
Note: do not worry about the content of in.disp, phana is driven by menu, one can get the
post-processing done by simply following the instructions.
And then use the gnuplot script file "plot.disp" to generate pdisp.eps:
-> gnuplot plot.disp
The resultant ``pdisp.eps'' compares the measured phonon dispersion to analytic solutions.
NOTE: the binary file provided here might be unreadable on some computers because of
incompatibility between different architectures.
The running of this example needs the molecule package included in lammps.
Author: Ling-Ti Kong, konglt@sjtu.edu.cn
Feb 2013

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examples/USER/phonon/1-1D-mono/data.pos Normal file
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16x1x1 (001) layers of simple cubic lattice
16 atoms
16 bonds
1 atom types
1 bond types
0.00000000 16.00000000 xlo xhi
-1.00000000 1.00000000 ylo yhi
-0.00010000 0.00010000 zlo zhi
Atoms
1 1 1 0.00000000 0.00000000 0.00000000
2 1 1 1.00000000 0.00000000 0.00000000
3 1 1 2.00000000 0.00000000 0.00000000
4 1 1 3.00000000 0.00000000 0.00000000
5 1 1 4.00000000 0.00000000 0.00000000
6 1 1 5.00000000 0.00000000 0.00000000
7 1 1 6.00000000 0.00000000 0.00000000
8 1 1 7.00000000 0.00000000 0.00000000
9 1 1 8.00000000 0.00000000 0.00000000
10 1 1 9.00000000 0.00000000 0.00000000
11 1 1 10.00000000 0.00000000 0.00000000
12 1 1 11.00000000 0.00000000 0.00000000
13 1 1 12.00000000 0.00000000 0.00000000
14 1 1 13.00000000 0.00000000 0.00000000
15 1 1 14.00000000 0.00000000 0.00000000
16 1 1 15.00000000 0.00000000 0.00000000
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
10 1 10 11
11 1 11 12
12 1 12 13
13 1 13 14
14 1 14 15
15 1 15 16
16 1 16 1
Bond Coeffs
1 0.5 1.0
Masses
1 1.0

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examples/USER/phonon/1-1D-mono/disp.dat Normal file
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# q qr freq
# 2pi/L 2pi/L sqrt(epsilon/(m.sigma^2)!
-0.5 0 0 0 1.97554
-0.4375 0 0 0.0625 1.97212
-0.375 0 0 0.125 1.84981
-0.3125 0 0 0.1875 1.65381
-0.25 0 0 0.25 1.3994
-0.1875 0 0 0.3125 1.11801
-0.125 0 0 0.375 0.771864
-0.0625 0 0 0.4375 0.40626
0 0 0 0.5 0
0.0625 0 0 0.5625 0.40626
0.125 0 0 0.625 0.771864
0.1875 0 0 0.6875 1.11801
0.25 0 0 0.75 1.3994
0.3125 0 0 0.8125 1.65381
0.375 0 0 0.875 1.84981
0.4375 0 0 0.9375 1.97212
0.5 0 0 1 1.97554

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examples/USER/phonon/1-1D-mono/in.Ana Normal file
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# 3D simple cubic lattice simulation
dimension 2
boundary p f p
units lj
atom_style bond
atom_modify sort 0 1.
bond_style harmonic
pair_style none
communicate single cutoff 2.0
# geometry
read_data data.pos
#
neighbor 0.5 nsq
neigh_modify delay 0 check no
#Langevin random seed
variable r equal 571101
#Langevin Temperature
variable t equal 0.005
# Langevin Damping variable
variable d equal 0.5
# time step
timestep 0.005
# Create velocities and equilibrate
compute MyTemp all temp/partial 1 0 0
velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp
velocity all set NULL 0.0 0.0 units box
#
fix 1 all langevin $t $t $d $r
fix_modify 1 temp MyTemp
fix 2 all setforce NULL 0. 0.
fix 3 all nve
fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1
fix_modify 4 temp MyTemp
#
# 1 2 3 4
thermo_style custom step temp pe etotal
thermo_modify temp MyTemp
thermo 100
dump 4 all atom 50000 dump_LJ_ANA.lammpstrj
run 2000000

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examples/USER/phonon/1-1D-mono/in.disp Normal file
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1
1
2
disp.dat
-0.5 0 0
0.5 0 0
17
q
0

146
examples/USER/phonon/1-1D-mono/log.lammps.example Normal file
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LAMMPS (21 Feb 2013)
# 3D simple cubic lattice simulation
dimension 2
boundary p f p
units lj
atom_style bond
atom_modify sort 0 1.
bond_style harmonic
pair_style none
communicate single cutoff 2.0
# geometry
read_data data.pos
1 = max bonds/atom
orthogonal box = (0 -1 -0.0001) to (16 1 0.0001)
1 by 1 by 1 MPI processor grid
16 atoms
16 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
#
neighbor 0.5 nsq
neigh_modify delay 0 check no
#Langevin random seed
variable r equal 571101
#Langevin Temperature
variable t equal 0.005
# Langevin Damping variable
variable d equal 0.5
# time step
timestep 0.005
# Create velocities and equilibrate
compute MyTemp all temp/partial 1 0 0
velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp
velocity all create 0.0050000000000000001041 28711 mom yes rot yes dist gaussian temp MyTemp
velocity all set NULL 0.0 0.0 units box
#
fix 1 all langevin $t $t $d $r
fix 1 all langevin 0.0050000000000000001041 $t $d $r
fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 $d $r
fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 $r
fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 571101
fix_modify 1 temp MyTemp
fix 2 all setforce NULL 0. 0.
fix 3 all nve
fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1
fix_modify 4 temp MyTemp
#
# 1 2 3 4
thermo_style custom step temp pe etotal
thermo_modify temp MyTemp
thermo 100
dump 4 all atom 50000 dump_LJ_ANA.lammpstrj
run 2000000
WARNING: Inconsistent image flags (domain.cpp:594)
Memory usage per processor = 1.91113 Mbytes
Step Temp PotEng TotEng
0 0.005 0 0.0021875
100 0.002868961 0.00049005558 0.001745226
200 0.0033995889 0.00054780054 0.0020351207
300 0.0054818055 0.0010469399 0.0034452298
400 0.0026493115 0.001228133 0.0023872068
500 0.0042074098 0.00093834909 0.0027790909
600 0.0057427721 0.00064844108 0.0031609039
700 0.004921032 0.0017780884 0.0039310399
800 0.0068003961 0.0021362756 0.0051114488
900 0.0031879644 0.0029121839 0.0043069184
...
1995500 0.0052867972 0.0024314544 0.0047444281
1995600 0.0061667626 0.00217977 0.0048777286
1995700 0.0089339997 0.0016799003 0.0055885252
1995800 0.0062354811 0.0027538517 0.0054818747
1995900 0.0047870661 0.0034792552 0.0055735966
1996000 0.0069073619 0.0026162915 0.0056382623
1996100 0.0055415014 0.0024814778 0.0049058847
1996200 0.0075113713 0.0025342419 0.0058204668
1996300 0.0036175152 0.0022876907 0.0038703536
1996400 0.0038697564 0.0019615869 0.0036546053
1996500 0.0047409774 0.0014638951 0.0035380727
1996600 0.0057706282 0.0016903471 0.004214997
1996700 0.0089467126 0.0019164807 0.0058306675
1996800 0.0049858554 0.0025648536 0.0047461653
1996900 0.0065316826 0.0018404119 0.004698023
1997000 0.0033658131 0.0013773556 0.0028498989
1997100 0.0055962484 0.0014630303 0.003911389
1997200 0.0040953065 0.001620329 0.0034120256
1997300 0.0047377588 0.0029475742 0.0050203437
1997400 0.0050964396 0.0032258218 0.0054555141
1997500 0.0044928787 0.0026156731 0.0045813076
1997600 0.0084888873 0.0020170995 0.0057309877
1997700 0.0018489614 0.0021713336 0.0029802542
1997800 0.00845042 0.0022370954 0.0059341542
1997900 0.0084259507 0.0034265784 0.0071129319
1998000 0.0035188519 0.0041636188 0.0057031165
1998100 0.00519759 0.0029875339 0.0052614795
1998200 0.0064780065 0.001261189 0.0040953169
1998300 0.0043427288 0.00068946033 0.0025894042
1998400 0.0043436101 0.00076392623 0.0026642556
1998500 0.0048600959 0.00046276456 0.0025890565
1998600 0.00400599 0.00083665093 0.0025892715
1998700 0.0047726401 0.0012718685 0.0033598985
1998800 0.0033232022 0.00096850115 0.0024224021
1998900 0.0040710536 0.0011903803 0.0029714662
1999000 0.0064288131 0.0011170182 0.0039296239
1999100 0.0032828285 0.0019236157 0.0033598532
1999200 0.0061845092 0.0016389768 0.0043446995
1999300 0.0056427996 0.0015509544 0.0040196792
1999400 0.0044191877 0.0013193707 0.0032527653
1999500 0.0050278316 0.001714613 0.0039142893
1999600 0.0088282478 0.0012904919 0.0051528503
1999700 0.0027763532 0.0012671682 0.0024818228
1999800 0.0031875782 0.0014186408 0.0028132062
1999900 0.0095469347 0.0012657077 0.0054424916
2000000 0.0050785787 0.0012610955 0.0034829737
Loop time of 11.2467 on 1 procs for 2000000 steps with 16 atoms
Pair time (%) = 0 (0)
Bond time (%) = 1.87007 (16.6277)
Neigh time (%) = 1.11974 (9.95616)
Comm time (%) = 1.64898 (14.6619)
Outpt time (%) = 0.0784338 (0.697395)
Other time (%) = 6.52945 (58.0568)
Nlocal: 16 ave 16 max 16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 6
Neighbor list builds = 2000000
Dangerous builds = 0

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examples/USER/phonon/1-1D-mono/map.in Normal file
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16 1 1 1
#l1 l2 l3 k atom_id
0 0 0 0 1
1 0 0 0 2
2 0 0 0 3
3 0 0 0 4
4 0 0 0 5
5 0 0 0 6
6 0 0 0 7
7 0 0 0 8
8 0 0 0 9
9 0 0 0 10
10 0 0 0 11
11 0 0 0 12
12 0 0 0 13
13 0 0 0 14
14 0 0 0 15
15 0 0 0 16

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examples/USER/phonon/1-1D-mono/pdisp.eps Normal file
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BIN
examples/USER/phonon/1-1D-mono/phonon.bin.2000000 Normal file
View File

Binary file not shown.

110
examples/USER/phonon/1-1D-mono/phonon.log Normal file
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@ -0,0 +1,110 @@
############################################################
# group name of the atoms under study : all
# total number of atoms in the group : 16
# dimension of the system : 1 D
# number of atoms per unit cell : 1
# dimension of the FFT mesh : 16 x 1 x 1
# number of wait steps before measurement : 500000
# frequency of GFC measurement : 10
# output result after this many measurement: 50000
# number of processors used by this run : 1
############################################################
# mapping information between lattice index and atom id
# nx ny nz nucell
16 1 1 1
# l1 l2 l3 k atom_id
0 0 0 0 1
1 0 0 0 2
2 0 0 0 3
3 0 0 0 4
4 0 0 0 5
5 0 0 0 6
6 0 0 0 7
7 0 0 0 8
8 0 0 0 9
9 0 0 0 10
10 0 0 0 11
11 0 0 0 12
12 0 0 0 13
13 0 0 0 14
14 0 0 0 15
15 0 0 0 16
############################################################
############################################################
# Current time step : 1000000
# Total number of measurements : 50000
# Average temperature of the measurement : 0.00497657
# Boltzmann constant under current units : 1
# basis vector A1 = [1 0 0]
# basis vector A2 = [0 2 0]
# basis vector A3 = [0 0 0.0002]
############################################################
# qx qy qz Phi(q)
0 0 0 0 0
0.0625 0 0 0.167273 0
0.125 0 0 0.607758 0
0.1875 0 0 1.27824 0
0.25 0 0 2.00811 0
0.3125 0 0 2.67802 0
0.375 0 0 3.48112 0
0.4375 0 0 3.7829 0
0.5 0 0 4.014 0
0.5625 0 0 3.7829 0
0.625 0 0 3.48112 0
0.6875 0 0 2.67802 0
0.75 0 0 2.00811 0
0.8125 0 0 1.27824 0
0.875 0 0 0.607758 0
0.9375 0 0 0.167273 0
############################################################
# Current time step : 1500000
# Total number of measurements : 100000
# Average temperature of the measurement : 0.00498233
# Boltzmann constant under current units : 1
# basis vector A1 = [1 0 0]
# basis vector A2 = [0 2 0]
# basis vector A3 = [0 0 0.0002]
############################################################
# qx qy qz Phi(q)
0 0 0 0 0
0.0625 0 0 0.171588 0
0.125 0 0 0.587006 0
0.1875 0 0 1.24373 0
0.25 0 0 1.9907 0
0.3125 0 0 2.71759 0
0.375 0 0 3.39634 0
0.4375 0 0 3.89609 0
0.5 0 0 3.83695 0
0.5625 0 0 3.89609 0
0.625 0 0 3.39634 0
0.6875 0 0 2.71759 0
0.75 0 0 1.9907 0
0.8125 0 0 1.24373 0
0.875 0 0 0.587006 0
0.9375 0 0 0.171588 0
############################################################
# Current time step : 2000000
# Total number of measurements : 150000
# Average temperature of the measurement : 0.00499855
# Boltzmann constant under current units : 1
# basis vector A1 = [1 0 0]
# basis vector A2 = [0 2 0]
# basis vector A3 = [0 0 0.0002]
############################################################
# qx qy qz Phi(q)
0 0 0 0 0
0.0625 0 0 0.165047 0
0.125 0 0 0.595774 0
0.1875 0 0 1.24996 0
0.25 0 0 1.95831 0
0.3125 0 0 2.73508 0
0.375 0 0 3.42181 0
0.4375 0 0 3.88925 0
0.5 0 0 3.90276 0
0.5625 0 0 3.88925 0
0.625 0 0 3.42181 0
0.6875 0 0 2.73508 0
0.75 0 0 1.95831 0
0.8125 0 0 1.24996 0
0.875 0 0 0.595774 0
0.9375 0 0 0.165047 0

20
examples/USER/phonon/1-1D-mono/plot.disp Normal file
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@ -0,0 +1,20 @@
m = 1.
k = 1.
# analytic solution for 1D monoatomic chain
omega(x) = 2.*sqrt(k/m) * abs(sin(pi*x))
set xlabel 'q'
set ylabel '{/Symbol w}'
set xr [-0.5:0.5]
set yr [0:2.5]
set format y '%.1f'
set term post enha color 20
set out 'pdisp.eps'
set key top left
set xtics ("-{/Symbol p}/a" -0.5, "{/Symbol G}" 0.0, "{/Symbol p}/a" 0.5)
set samples 101
set grid xtics lt 9
plot omega(x) w l lt 1 lc 3 t 'Theory', 'disp.dat' u 1:5 w p pt 7 ps 1.0 lc 1 t 'MD'

37
examples/USER/phonon/2-1D-diatomic/README Normal file
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@ -0,0 +1,37 @@
This directory illustrates the usage of fix-phonon to calculate the dynamical
matrix as well as phonon dispersion curve for 1 dimensional diatomic chain.
The files under this directory:
1) data.pos : LAMMPS input file
2) disp.dat : phonon dispersion data from phonon.bin.2000000
3) in.Ana : LAMMPS input file
4) in.disp : input file to get disp.dat by phana
5) log.lammps : LAMMPS log file
6) map.in : LAMMPS input file for fix-phonon
7) pdisp.eps : phonon dispersion for 1D monoatomic chain, generated by plot.disp
8) phonon.bin.2000000 : last output binary file by fix-phonon
9) phonon.log : log file for fix-phonon
10) plot.disp : script to generate phonon dispersion curve
11) README : this file
To run this example, simply:
-> lmp -in in.Ana -screen none
Once done, one can use the auxiliary analysing code "phana" to obtain "disp.dat" based on
data from phonon.bin.2000000:
-> phana phonon.bin.2000000 < in.disp
And then use the gnuplot script file "plot.disp" to generate pdisp.eps:
-> gnuplot plot.disp
The resultant ``pdisp.eps'' compares the measured phonon dispersion to analytic solutions.
NOTE: the binary file provided here might be unreadable on some computers because of
incompatibility between different architectures.
The running of this example needs the molecule package included in lammps.
Author: Ling-Ti Kong, konglt@sjtu.edu.cn
Feb 2013

154
examples/USER/phonon/2-1D-diatomic/data.pos Normal file
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64x1x1 (001) layers of simple cubic lattice
64 atoms
64 bonds
2 atom types
1 bond types
0.00000000 64.00000000 xlo xhi
0.00000000 1.00000000 ylo yhi
0.00000000 1.00000000 zlo zhi
Atoms
1 1 1 0.00000000 0.00000000 0.00000000
2 1 2 1.00000000 0.00000000 0.00000000
3 1 1 2.00000000 0.00000000 0.00000000
4 1 2 3.00000000 0.00000000 0.00000000
5 1 1 4.00000000 0.00000000 0.00000000
6 1 2 5.00000000 0.00000000 0.00000000
7 1 1 6.00000000 0.00000000 0.00000000
8 1 2 7.00000000 0.00000000 0.00000000
9 1 1 8.00000000 0.00000000 0.00000000
10 1 2 9.00000000 0.00000000 0.00000000
11 1 1 10.00000000 0.00000000 0.00000000
12 1 2 11.00000000 0.00000000 0.00000000
13 1 1 12.00000000 0.00000000 0.00000000
14 1 2 13.00000000 0.00000000 0.00000000
15 1 1 14.00000000 0.00000000 0.00000000
16 1 2 15.00000000 0.00000000 0.00000000
17 1 1 16.00000000 0.00000000 0.00000000
18 1 2 17.00000000 0.00000000 0.00000000
19 1 1 18.00000000 0.00000000 0.00000000
20 1 2 19.00000000 0.00000000 0.00000000
21 1 1 20.00000000 0.00000000 0.00000000
22 1 2 21.00000000 0.00000000 0.00000000
23 1 1 22.00000000 0.00000000 0.00000000
24 1 2 23.00000000 0.00000000 0.00000000
25 1 1 24.00000000 0.00000000 0.00000000
26 1 2 25.00000000 0.00000000 0.00000000
27 1 1 26.00000000 0.00000000 0.00000000
28 1 2 27.00000000 0.00000000 0.00000000
29 1 1 28.00000000 0.00000000 0.00000000
30 1 2 29.00000000 0.00000000 0.00000000
31 1 1 30.00000000 0.00000000 0.00000000
32 1 2 31.00000000 0.00000000 0.00000000
33 1 1 32.00000000 0.00000000 0.00000000
34 1 2 33.00000000 0.00000000 0.00000000
35 1 1 34.00000000 0.00000000 0.00000000
36 1 2 35.00000000 0.00000000 0.00000000
37 1 1 36.00000000 0.00000000 0.00000000
38 1 2 37.00000000 0.00000000 0.00000000
39 1 1 38.00000000 0.00000000 0.00000000
40 1 2 39.00000000 0.00000000 0.00000000
41 1 1 40.00000000 0.00000000 0.00000000
42 1 2 41.00000000 0.00000000 0.00000000
43 1 1 42.00000000 0.00000000 0.00000000
44 1 2 43.00000000 0.00000000 0.00000000
45 1 1 44.00000000 0.00000000 0.00000000
46 1 2 45.00000000 0.00000000 0.00000000
47 1 1 46.00000000 0.00000000 0.00000000
48 1 2 47.00000000 0.00000000 0.00000000
49 1 1 48.00000000 0.00000000 0.00000000
50 1 2 49.00000000 0.00000000 0.00000000
51 1 1 50.00000000 0.00000000 0.00000000
52 1 2 51.00000000 0.00000000 0.00000000
53 1 1 52.00000000 0.00000000 0.00000000
54 1 2 53.00000000 0.00000000 0.00000000
55 1 1 54.00000000 0.00000000 0.00000000
56 1 2 55.00000000 0.00000000 0.00000000
57 1 1 56.00000000 0.00000000 0.00000000
58 1 2 57.00000000 0.00000000 0.00000000
59 1 1 58.00000000 0.00000000 0.00000000
60 1 2 59.00000000 0.00000000 0.00000000
61 1 1 60.00000000 0.00000000 0.00000000
62 1 2 61.00000000 0.00000000 0.00000000
63 1 1 62.00000000 0.00000000 0.00000000
64 1 2 63.00000000 0.00000000 0.00000000
Bonds
1 1 1 2
2 1 1 64
3 1 2 3
4 1 3 4
5 1 4 5
6 1 5 6
7 1 6 7
8 1 7 8
9 1 8 9
10 1 9 10
11 1 10 11
12 1 11 12
13 1 12 13
14 1 13 14
15 1 14 15
16 1 15 16
17 1 16 17
18 1 17 18
19 1 18 19
20 1 19 20
21 1 20 21
22 1 21 22
23 1 22 23
24 1 23 24
25 1 24 25
26 1 25 26
27 1 26 27
28 1 27 28
29 1 28 29
30 1 29 30
31 1 30 31
32 1 31 32
33 1 32 33
34 1 33 34
35 1 34 35
36 1 35 36
37 1 36 37
38 1 37 38
39 1 38 39
40 1 39 40
41 1 40 41
42 1 41 42
43 1 42 43
44 1 43 44
45 1 44 45
46 1 45 46
47 1 46 47
48 1 47 48
49 1 48 49
50 1 49 50
51 1 50 51
52 1 51 52
53 1 52 53
54 1 53 54
55 1 54 55
56 1 55 56
57 1 56 57
58 1 57 58
59 1 58 59
60 1 59 60
61 1 60 61
62 1 61 62
63 1 62 63
64 1 63 64
Bond Coeffs
1 0.5 1.0
Masses
1 1.0
2 2.0

35
examples/USER/phonon/2-1D-diatomic/disp.dat Normal file
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# q qr freq
# 2pi/L 2pi/L sqrt(epsilon/(m.sigma^2)!
-0.5 0 0 0 0.984716 1.41168
-0.46875 0 0 0.03125 1.00625 1.43003
-0.4375 0 0 0.0625 0.973905 1.43204
-0.40625 0 0 0.09375 0.943149 1.45641
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-0.28125 0 0 0.21875 0.68801 1.58621
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-0.1875 0 0 0.3125 0.477876 1.6563
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0 0 0 0.5 1.05367e-08 1.72979
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46
examples/USER/phonon/2-1D-diatomic/in.Ana Normal file
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# 3D simple cubic lattice simulation
dimension 2
boundary p f p
units lj
atom_style bond
atom_modify sort 0 1.
bond_style harmonic
pair_style none
communicate single cutoff 2.0
# geometry
read_data data.pos
#
neighbor 1.0 nsq
neigh_modify delay 0 check no
#Langevin random seed
variable r equal 571101
#Langevin Temperature
variable t equal 0.005
# Langevin Damping variable
variable d equal 0.5
# Create velocities and equilibrate
compute MyTemp all temp/partial 1 0 0
velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp
velocity all set NULL 0.0 0.0 units box
#
fix 1 all langevin $t $t $d $r
fix_modify 1 temp MyTemp
fix 2 all setforce NULL 0. 0.
fix 3 all nve
fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1
fix_modify 4 temp MyTemp
# 1 2 3 4
thermo_style custom step temp pe etotal
thermo_modify temp MyTemp
thermo 100
#
run 2000000

9
examples/USER/phonon/2-1D-diatomic/in.disp Normal file
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10
1
2
disp.dat
-0.5 0 0
0.5 0 0
33
q
0

113
examples/USER/phonon/2-1D-diatomic/log.lammps.example Normal file
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LAMMPS (21 Feb 2013)
# 3D simple cubic lattice simulation
dimension 2
boundary p f p
units lj
atom_style bond
atom_modify sort 0 1.
bond_style harmonic
pair_style none
communicate single cutoff 2.0
# geometry
read_data data.pos
2 = max bonds/atom
orthogonal box = (0 0 0) to (64 1 1)
1 by 1 by 1 MPI processor grid
64 atoms
64 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
#
neighbor 1.0 nsq
neigh_modify delay 0 check no
#Langevin random seed
variable r equal 571101
#Langevin Temperature
variable t equal 0.005
# Langevin Damping variable
variable d equal 0.5
# Create velocities and equilibrate
compute MyTemp all temp/partial 1 0 0
velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp
velocity all create 0.0050000000000000001041 28711 mom yes rot yes dist gaussian temp MyTemp
velocity all set NULL 0.0 0.0 units box
#
fix 1 all langevin $t $t $d $r
fix 1 all langevin 0.0050000000000000001041 $t $d $r
fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 $d $r
fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 $r
fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 571101
fix_modify 1 temp MyTemp
fix 2 all setforce NULL 0. 0.
fix 3 all nve
fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1
fix_modify 4 temp MyTemp
# 1 2 3 4
thermo_style custom step temp pe etotal
thermo_modify temp MyTemp
thermo 100
#
run 2000000
Memory usage per processor = 2.01061 Mbytes
Step Temp PotEng TotEng
0 0.005 0 0.002421875
100 0.0044233185 0.00069227571 0.0028348206
200 0.0051557212 0.0012425996 0.003739902
300 0.004357315 0.0012750554 0.0033856298
400 0.0048269093 0.0014376622 0.0037756964
500 0.0047025425 0.0016352541 0.0039130482
600 0.0054651713 0.0016709504 0.0043181428
700 0.0053552729 0.0018353947 0.0044293551
800 0.005954909 0.0019755263 0.0048599354
900 0.0042057592 0.0023020508 0.0043392155
1000 0.0057669621 0.0025897902 0.0053831625
...
1998400 0.0063659105 0.0026460546 0.0057295425
1998500 0.0043373725 0.0027045125 0.0048054273
1998600 0.0048756101 0.0024999167 0.0048615404
1998700 0.0046508855 0.0023965866 0.0046493593
1998800 0.0062661518 0.0022217336 0.0052569009
1998900 0.0061555738 0.0023546222 0.0053362283
1999000 0.0043069574 0.0024786217 0.0045648042
1999100 0.0055141568 0.0028549884 0.0055259081
1999200 0.0034372635 0.0027990632 0.0044639877
1999300 0.0048351937 0.0023526277 0.0046946746
1999400 0.0057087851 0.0020335116 0.0047987044
1999500 0.0033912965 0.0023030393 0.0039456986
1999600 0.0054813169 0.0023096891 0.004964702
1999700 0.0048389727 0.0021943385 0.0045382159
1999800 0.0059277298 0.0020055057 0.0048767498
1999900 0.0059290305 0.002299977 0.0051718512
2000000 0.0047343315 0.0026625608 0.0049557526
Loop time of 32.3665 on 1 procs for 2000000 steps with 64 atoms
Pair time (%) = 0 (0)
Bond time (%) = 6.21905 (19.2145)
Neigh time (%) = 3.25312 (10.0509)
Comm time (%) = 3.04437 (9.40594)
Outpt time (%) = 0.0748212 (0.231169)
Other time (%) = 19.7751 (61.0975)
Nlocal: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 6
Neighbor list builds = 2000000
Dangerous builds = 0

66
examples/USER/phonon/2-1D-diatomic/map.in Normal file
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32 1 1 2
#l1 l2 l3 k tag
0 0 0 0 1
0 0 0 1 2
1 0 0 0 3
1 0 0 1 4
2 0 0 0 5
2 0 0 1 6
3 0 0 0 7
3 0 0 1 8
4 0 0 0 9
4 0 0 1 10
5 0 0 0 11
5 0 0 1 12
6 0 0 0 13
6 0 0 1 14
7 0 0 0 15
7 0 0 1 16
8 0 0 0 17
8 0 0 1 18
9 0 0 0 19
9 0 0 1 20
10 0 0 0 21
10 0 0 1 22
11 0 0 0 23
11 0 0 1 24
12 0 0 0 25
12 0 0 1 26
13 0 0 0 27
13 0 0 1 28
14 0 0 0 29
14 0 0 1 30
15 0 0 0 31
15 0 0 1 32
16 0 0 0 33
16 0 0 1 34
17 0 0 0 35
17 0 0 1 36
18 0 0 0 37
18 0 0 1 38
19 0 0 0 39
19 0 0 1 40
20 0 0 0 41
20 0 0 1 42
21 0 0 0 43
21 0 0 1 44
22 0 0 0 45
22 0 0 1 46
23 0 0 0 47
23 0 0 1 48
24 0 0 0 49
24 0 0 1 50
25 0 0 0 51
25 0 0 1 52
26 0 0 0 53
26 0 0 1 54
27 0 0 0 55
27 0 0 1 56
28 0 0 0 57
28 0 0 1 58
29 0 0 0 59
29 0 0 1 60
30 0 0 0 61
30 0 0 1 62
31 0 0 0 63
31 0 0 1 64

924
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<< Tile8x8
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>> matrix makepattern
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<< Tile8x8
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>> matrix makepattern
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<< Tile8x8
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>> matrix makepattern
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<< Tile8x8
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>> matrix makepattern
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<< Tile8x8
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>> matrix makepattern
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<< Tile8x8
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>> matrix makepattern
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<< Tile8x8
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>> matrix makepattern
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} def
%
%
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%
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%
% Substitute for Level 2 pattern fill codes with
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%
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203
examples/USER/phonon/2-1D-diatomic/pdos.dat Normal file
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@ -0,0 +1,203 @@
# frequency DOS
#sqrt(epsilon/(m.sigma^2)! number
0 0.154847
0.01 0.247755
0.02 0.247755
0.03 0.309693
0.04 0.309693
0.05 0.309693
0.06 0.309693
0.07 0.371632
0.08 0.371632
0.09 0.433571
0.1 0.495509
0.11 0.557448
0.12 0.495509
0.13 0.495509
0.14 0.495509
0.15 0.495509
0.16 0.433571
0.17 0.433571
0.18 0.433571
0.19 0.433571
0.2 0.433571
0.21 0.371632
0.22 0.433571
0.23 0.371632
0.24 0.371632
0.25 0.371632
0.26 0.433571
0.27 0.371632
0.28 0.371632
0.29 0.371632
0.3 0.371632
0.31 0.371632
0.32 0.371632
0.33 0.309693
0.34 0.371632
0.35 0.371632
0.36 0.371632
0.37 0.371632
0.38 0.433571
0.39 0.371632
0.4 0.371632
0.41 0.371632
0.42 0.371632
0.43 0.309693
0.44 0.371632
0.45 0.371632
0.46 0.433571
0.47 0.371632
0.48 0.495509
0.49 0.557448
0.5 0.681325
0.51 0.619387
0.52 0.495509
0.53 0.433571
0.54 0.371632
0.55 0.371632
0.56 0.309693
0.57 0.309693
0.58 0.309693
0.59 0.309693
0.6 0.371632
0.61 0.309693
0.62 0.371632
0.63 0.433571
0.64 0.495509
0.65 0.495509
0.66 0.495509
0.67 0.557448
0.68 0.495509
0.69 0.495509
0.7 0.433571
0.71 0.495509
0.72 0.433571
0.73 0.433571
0.74 0.495509
0.75 0.495509
0.76 0.495509
0.77 0.495509
0.78 0.557448
0.79 0.495509
0.8 0.557448
0.81 0.557448
0.82 0.495509
0.83 0.495509
0.84 0.495509
0.85 0.557448
0.86 0.495509
0.87 0.495509
0.88 0.433571
0.89 0.433571
0.9 0.433571
0.91 0.371632
0.92 0.495509
0.93 0.433571
0.94 0.557448
0.95 0.805203
0.96 1.17683
0.97 1.1149
0.98 1.02199
0.99 1.98204
1 2.10592
1.01 0.991019
1.02 0
1.03 0
1.04 0
1.05 0
1.06 0
1.07 0
1.08 0
1.09 0
1.1 0
1.11 0
1.12 0
1.13 0
1.14 0
1.15 0
1.16 0
1.17 0
1.18 0
1.19 0
1.2 0
1.21 0
1.22 0
1.23 0
1.24 0
1.25 0
1.26 0
1.27 0
1.28 0
1.29 0
1.3 0
1.31 0
1.32 0
1.33 0
1.34 0
1.35 0
1.36 0
1.37 0
1.38 0
1.39 0
1.4 0
1.41 0.96005
1.42 1.30071
1.43 4.52152
1.44 1.36265
1.45 0.991019
1.46 0.92908
1.47 0.805203
1.48 0.743264
1.49 0.743264
1.5 0.681325
1.51 0.619387
1.52 0.619387
1.53 0.619387
1.54 0.92908
1.55 2.22979
1.56 1.36265
1.57 0.991019
1.58 1.1149
1.59 1.9201
1.6 1.42459
1.61 0.743264
1.62 0.619387
1.63 0.557448
1.64 0.743264
1.65 3.28275
1.66 0.743264
1.67 0.495509
1.68 0.495509
1.69 0.495509
1.7 3.34469
1.71 3.46857
1.72 3.5305
1.73 2.81821
1.74 3.34469
1.75 0
1.76 0
1.77 0
1.78 0
1.79 0
1.8 0
1.81 0
1.82 0
1.83 0
1.84 0
1.85 0
1.86 0
1.87 0
1.88 0
1.89 0
1.9 0
1.91 0
1.92 0
1.93 0
1.94 0
1.95 0
1.96 0
1.97 0
1.98 0
1.99 0
2 0

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examples/USER/phonon/2-1D-diatomic/phonon.bin.2000000 Normal file
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206
examples/USER/phonon/2-1D-diatomic/phonon.log Normal file
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############################################################
# group name of the atoms under study : all
# total number of atoms in the group : 64
# dimension of the system : 1 D
# number of atoms per unit cell : 2
# dimension of the FFT mesh : 32 x 1 x 1
# number of wait steps before measurement : 500000
# frequency of GFC measurement : 10
# output result after this many measurement: 50000
# number of processors used by this run : 1
############################################################
# mapping information between lattice index and atom id
# nx ny nz nucell
32 1 1 2
# l1 l2 l3 k atom_id
0 0 0 0 1
0 0 0 1 2
1 0 0 0 3
1 0 0 1 4
2 0 0 0 5
2 0 0 1 6
3 0 0 0 7
3 0 0 1 8
4 0 0 0 9
4 0 0 1 10
5 0 0 0 11
5 0 0 1 12
6 0 0 0 13
6 0 0 1 14
7 0 0 0 15
7 0 0 1 16
8 0 0 0 17
8 0 0 1 18
9 0 0 0 19
9 0 0 1 20
10 0 0 0 21
10 0 0 1 22
11 0 0 0 23
11 0 0 1 24
12 0 0 0 25
12 0 0 1 26
13 0 0 0 27
13 0 0 1 28
14 0 0 0 29
14 0 0 1 30
15 0 0 0 31
15 0 0 1 32
16 0 0 0 33
16 0 0 1 34
17 0 0 0 35
17 0 0 1 36
18 0 0 0 37
18 0 0 1 38
19 0 0 0 39
19 0 0 1 40
20 0 0 0 41
20 0 0 1 42
21 0 0 0 43
21 0 0 1 44
22 0 0 0 45
22 0 0 1 46
23 0 0 0 47
23 0 0 1 48
24 0 0 0 49
24 0 0 1 50
25 0 0 0 51
25 0 0 1 52
26 0 0 0 53
26 0 0 1 54
27 0 0 0 55
27 0 0 1 56
28 0 0 0 57
28 0 0 1 58
29 0 0 0 59
29 0 0 1 60
30 0 0 0 61
30 0 0 1 62
31 0 0 0 63
31 0 0 1 64
############################################################
############################################################
# Current time step : 1000000
# Total number of measurements : 50000
# Average temperature of the measurement : 0.00499889
# Boltzmann constant under current units : 1
# basis vector A1 = [2 0 0]
# basis vector A2 = [0 1 0]
# basis vector A3 = [0 0 1]
############################################################
# qx qy qz Phi(q)
0 0 0 2.0269 0 -1.43323 0 -1.43323 0 1.01345 0
0.03125 0 0 2.06958 0 -1.44367 0.144297 -1.44367 -0.144297 1.03745 0
0.0625 0 0 2.00734 -7.10386e-17 -1.36818 0.273607 -1.36818 -0.273607 1.02097 0
0.09375 0 0 2.06033 7.36546e-16 -1.32894 0.389454 -1.32894 -0.389454 1.00889 3.19674e-16
0.125 0 0 2.04516 7.25738e-16 -1.20961 0.516478 -1.20961 -0.516478 1.0073 2.84154e-16
0.15625 0 0 2.05756 0 -1.12954 0.615757 -1.12954 -0.615757 1.02862 0
0.1875 0 0 2.01319 0 -0.970491 0.627631 -0.970491 -0.627631 0.998014 0
0.21875 0 0 1.92269 1.42077e-16 -0.863486 0.66779 -0.863486 -0.66779 1.00343 8.73509e-17
0.25 0 0 1.99044 1.71855e-16 -0.671658 0.661397 -0.671658 -0.661397 0.956893 7.10386e-17
0.28125 0 0 1.96341 -7.10386e-17 -0.556809 0.66713 -0.556809 -0.66713 0.987126 4.2268e-17
0.3125 0 0 2.04354 0 -0.442943 0.661601 -0.442943 -0.661601 0.961726 1.77596e-17
0.34375 0 0 1.98412 0 -0.313464 0.632666 -0.313464 -0.632666 1.01134 -2.21836e-17
0.375 0 0 2.00509 2.17993e-17 -0.187554 0.499349 -0.187554 -0.499349 0.953607 -8.87982e-18
0.40625 0 0 1.91679 0 -0.0962947 0.408121 -0.0962947 -0.408121 1.02919 0
0.4375 0 0 1.98963 0 -0.0137565 0.277826 -0.0137565 -0.277826 1.01624 0
0.46875 0 0 2.08228 0 -0.0312083 0.0872272 -0.0312083 -0.0872272 0.991567 0
0.5 0 0 1.95481 0 0.0542224 0 0.0542224 0 1.00583 0
0.53125 0 0 2.08228 0 -0.0312083 -0.0872272 -0.0312083 0.0872272 0.991567 0
0.5625 0 0 1.98963 0 -0.0137565 -0.277826 -0.0137565 0.277826 1.01624 0
0.59375 0 0 1.91679 0 -0.0962947 -0.408121 -0.0962947 0.408121 1.02919 0
0.625 0 0 2.00509 -2.17993e-17 -0.187554 -0.499349 -0.187554 0.499349 0.953607 8.87982e-18
0.65625 0 0 1.98412 0 -0.313464 -0.632666 -0.313464 0.632666 1.01134 2.21836e-17
0.6875 0 0 2.04354 0 -0.442943 -0.661601 -0.442943 0.661601 0.961726 -1.77596e-17
0.71875 0 0 1.96341 7.10386e-17 -0.556809 -0.66713 -0.556809 0.66713 0.987126 -4.2268e-17
0.75 0 0 1.99044 -1.71855e-16 -0.671658 -0.661397 -0.671658 0.661397 0.956893 -7.10386e-17
0.78125 0 0 1.92269 -1.42077e-16 -0.863486 -0.66779 -0.863486 0.66779 1.00343 -8.73509e-17
0.8125 0 0 2.01319 0 -0.970491 -0.627631 -0.970491 0.627631 0.998014 0
0.84375 0 0 2.05756 0 -1.12954 -0.615757 -1.12954 0.615757 1.02862 0
0.875 0 0 2.04516 -7.25738e-16 -1.20961 -0.516478 -1.20961 0.516478 1.0073 -2.84154e-16
0.90625 0 0 2.06033 -7.36546e-16 -1.32894 -0.389454 -1.32894 0.389454 1.00889 -3.19674e-16
0.9375 0 0 2.00734 7.10386e-17 -1.36818 -0.273607 -1.36818 0.273607 1.02097 0
0.96875 0 0 2.06958 0 -1.44367 -0.144297 -1.44367 0.144297 1.03745 0
############################################################
# Current time step : 1500000
# Total number of measurements : 100000
# Average temperature of the measurement : 0.00499969
# Boltzmann constant under current units : 1
# basis vector A1 = [2 0 0]
# basis vector A2 = [0 1 0]
# basis vector A3 = [0 0 1]
############################################################
# qx qy qz Phi(q)
0 0 0 2.00227 0 -1.41582 0 -1.41582 0 1.00114 0
0.03125 0 0 2.06839 -2.94857e-15 -1.44775 0.141336 -1.44775 -0.141336 1.03568 -1.48867e-15
0.0625 0 0 1.99449 0 -1.35985 0.267438 -1.35985 -0.267438 0.997747 0
0.09375 0 0 2.01906 7.07225e-16 -1.30258 0.390432 -1.30258 -0.390432 1.00279 3.55249e-16
0.125 0 0 2.0047 0 -1.19787 0.503497 -1.19787 -0.503497 1.00067 -3.55249e-17
0.15625 0 0 2.05042 4.26299e-16 -1.12849 0.613659 -1.12849 -0.613659 1.03457 1.85685e-16
0.1875 0 0 1.99151 0 -0.971684 0.625667 -0.971684 -0.625667 0.990665 0
0.21875 0 0 1.96519 -7.10498e-17 -0.861495 0.687109 -0.861495 -0.687109 1.0008 0
0.25 0 0 2.01865 0 -0.687312 0.684014 -0.687312 -0.684014 0.977055 0
0.28125 0 0 1.9933 0 -0.560168 0.698726 -0.560168 -0.698726 1.00805 -4.40715e-17
0.3125 0 0 2.01323 0 -0.446505 0.648764 -0.446505 -0.648764 1.00283 -1.77625e-17
0.34375 0 0 2.00398 0 -0.313827 0.630741 -0.313827 -0.630741 0.996834 0
0.375 0 0 2.0191 0 -0.216211 0.499651 -0.216211 -0.499651 0.978322 0
0.40625 0 0 1.97734 -4.44061e-18 -0.102328 0.398954 -0.102328 -0.398954 1.03793 0
0.4375 0 0 1.99332 -2.22031e-18 -0.0639782 0.238226 -0.0639782 -0.238226 1.00811 -1.3774e-18
0.46875 0 0 2.02854 0 -0.0151203 0.0911116 -0.0151203 -0.0911116 1.00593 0
0.5 0 0 1.99466 0 0.0671755 0 0.0671755 0 0.967275 0
0.53125 0 0 2.02854 0 -0.0151203 -0.0911116 -0.0151203 0.0911116 1.00593 0
0.5625 0 0 1.99332 2.22031e-18 -0.0639782 -0.238226 -0.0639782 0.238226 1.00811 1.3774e-18
0.59375 0 0 1.97734 4.44061e-18 -0.102328 -0.398954 -0.102328 0.398954 1.03793 0
0.625 0 0 2.0191 0 -0.216211 -0.499651 -0.216211 0.499651 0.978322 0
0.65625 0 0 2.00398 0 -0.313827 -0.630741 -0.313827 0.630741 0.996834 0
0.6875 0 0 2.01323 0 -0.446505 -0.648764 -0.446505 0.648764 1.00283 1.77625e-17
0.71875 0 0 1.9933 0 -0.560168 -0.698726 -0.560168 0.698726 1.00805 4.40715e-17
0.75 0 0 2.01865 0 -0.687312 -0.684014 -0.687312 0.684014 0.977055 0
0.78125 0 0 1.96519 7.10498e-17 -0.861495 -0.687109 -0.861495 0.687109 1.0008 0
0.8125 0 0 1.99151 0 -0.971684 -0.625667 -0.971684 0.625667 0.990665 0
0.84375 0 0 2.05042 -4.26299e-16 -1.12849 -0.613659 -1.12849 0.613659 1.03457 -1.85685e-16
0.875 0 0 2.0047 0 -1.19787 -0.503497 -1.19787 0.503497 1.00067 3.55249e-17
0.90625 0 0 2.01906 -7.07225e-16 -1.30258 -0.390432 -1.30258 0.390432 1.00279 -3.55249e-16
0.9375 0 0 1.99449 0 -1.35985 -0.267438 -1.35985 0.267438 0.997747 0
0.96875 0 0 2.06839 2.94857e-15 -1.44775 -0.141336 -1.44775 0.141336 1.03568 1.48867e-15
############################################################
# Current time step : 2000000
# Total number of measurements : 150000
# Average temperature of the measurement : 0.00499897
# Boltzmann constant under current units : 1
# basis vector A1 = [2 0 0]
# basis vector A2 = [0 1 0]
# basis vector A3 = [0 0 1]
############################################################
# qx qy qz Phi(q)
0 0 0 1.99479 0 -1.41053 0 -1.41053 0 0.997396 0
0.03125 0 0 2.03068 0 -1.41965 0.138345 -1.41965 -0.138345 1.0155 0
0.0625 0 0 1.99892 7.10396e-17 -1.36162 0.269053 -1.36162 -0.269053 1.00066 0
0.09375 0 0 2.00599 0 -1.29893 0.389829 -1.29893 -0.389829 0.995323 0
0.125 0 0 1.991 6.87803e-16 -1.20232 0.495552 -1.20232 -0.495552 0.991252 2.84159e-16
0.15625 0 0 2.05187 1.42079e-16 -1.12612 0.617447 -1.12612 -0.617447 1.02736 0
0.1875 0 0 1.97476 7.10396e-17 -0.972012 0.630423 -0.972012 -0.630423 0.996946 0
0.21875 0 0 2.00314 0 -0.862555 0.695244 -0.862555 -0.695244 0.999215 0
0.25 0 0 1.9755 0 -0.69573 0.680591 -0.69573 -0.680591 0.988546 0
0.28125 0 0 1.99393 0 -0.560979 0.692292 -0.560979 -0.692292 0.995507 -3.55198e-17
0.3125 0 0 2.00817 0 -0.436753 0.642127 -0.436753 -0.642127 0.989051 0
0.34375 0 0 2.02348 0 -0.310766 0.620888 -0.310766 -0.620888 1.01631 0
0.375 0 0 2.01177 0 -0.213987 0.483325 -0.213987 -0.483325 0.98933 0
0.40625 0 0 1.97394 0 -0.116509 0.382146 -0.116509 -0.382146 1.03672 0
0.4375 0 0 1.98656 0 -0.0609164 0.250798 -0.0609164 -0.250798 1.01266 1.39007e-18
0.46875 0 0 2.03013 0 -0.0242785 0.120597 -0.0242785 -0.120597 1.02741 1.78858e-19
0.5 0 0 1.98872 0 0.0648313 0 0.0648313 0 0.973791 0
0.53125 0 0 2.03013 0 -0.0242785 -0.120597 -0.0242785 0.120597 1.02741 -1.78858e-19
0.5625 0 0 1.98656 0 -0.0609164 -0.250798 -0.0609164 0.250798 1.01266 -1.39007e-18
0.59375 0 0 1.97394 0 -0.116509 -0.382146 -0.116509 0.382146 1.03672 0
0.625 0 0 2.01177 0 -0.213987 -0.483325 -0.213987 0.483325 0.98933 0
0.65625 0 0 2.02348 0 -0.310766 -0.620888 -0.310766 0.620888 1.01631 0
0.6875 0 0 2.00817 0 -0.436753 -0.642127 -0.436753 0.642127 0.989051 0
0.71875 0 0 1.99393 0 -0.560979 -0.692292 -0.560979 0.692292 0.995507 3.55198e-17
0.75 0 0 1.9755 0 -0.69573 -0.680591 -0.69573 0.680591 0.988546 0
0.78125 0 0 2.00314 0 -0.862555 -0.695244 -0.862555 0.695244 0.999215 0
0.8125 0 0 1.97476 -7.10396e-17 -0.972012 -0.630423 -0.972012 0.630423 0.996946 0
0.84375 0 0 2.05187 -1.42079e-16 -1.12612 -0.617447 -1.12612 0.617447 1.02736 0
0.875 0 0 1.991 -6.87803e-16 -1.20232 -0.495552 -1.20232 0.495552 0.991252 -2.84159e-16
0.90625 0 0 2.00599 0 -1.29893 -0.389829 -1.29893 0.389829 0.995323 0
0.9375 0 0 1.99892 -7.10396e-17 -1.36162 -0.269053 -1.36162 0.269053 1.00066 0
0.96875 0 0 2.03068 0 -1.41965 -0.138345 -1.41965 0.138345 1.0155 0

25
examples/USER/phonon/2-1D-diatomic/plot.disp Normal file
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m = 1.
M = 2.
k = 1.
omp(x) = sqrt( k*(m+M)/(m*M)*(1. + (1.-4*m*M/(m+M)**2*(sin(pi*x))**2)**0.5))
omm(x) = sqrt( k*(m+M)/(m*M)*(1. - (1.-4*m*M/(m+M)**2*(sin(pi*x))**2)**0.5))
set xlabel 'q'
set ylabel '{/Symbol w}'
set xr [-0.5:0.5]
set yr [0:2.0]
set format y '%.1f'
set term post enha color 20
set out 'pdisp.eps'
set key top left
set xtics ("-{/Symbol p}/2a" -0.5, "{/Symbol G}" 0.0, "{/Symbol p}/2a" 0.5)
set samples 101
set grid xtics lt 9
plot omp(x) w l lt 1 lc 3 t 'Theory',\
omm(x) w l lt 1 lc 3 t '',\
'disp.dat' u 1:5 w p pt 7 ps 1.0 lt 1 t 'MD',\
'' u 1:6 w p pt 7 ps 1.0 lt 1 t ''

BIN
examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 Normal file
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1575
examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log.example Normal file
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examples/USER/phonon/3-3D-FCC-Cu-EAM/README Normal file
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This directory illustrates the usage of fix-phonon to calculate the dynamical
matrix as well as phonon dispersion curve for FCC Cu based on EAM potentail.
The files under this directory:
1) CuPhonon.bin.6500000 : last output binary file by fix-phonon
2) CuPhonon.log : log file for fix-phonon
3) cuu3.eam : EAM potential file for Cu
4) data.pos : LAMMPS input file
5) disp.dat : phonon dispersion data from CuPhonon.bin.6500000
6) disp-expr.dat : experimental phonon dispersion data for Cu
7) disp-ld.dat : phonon dispersion data by lattice dynamics based on EAM
8) dos.dat : phonon DOS data from CuPhonon.bin.6500000
9) dos-expr.dat : experimental PDOS for Cu
10) dos-ld.dat : PDOS by LD based on EAM
11) in.disp : input file to get disp.dat by phana
12) in.dos : input file to get dos.dat by phana
13) in.EAM3D : LAMMPS input file
14) log.lammps : LAMMPS log file
15) map.in : LAMMPS input file for fix-phonon
16) pdisp.eps : figure of phonon dispersion curves
17) pdos.eps : figure of phonon density of states
18) plot.disp : gnuplot script to generate pdisp.eps
19) plot.dos : gnuplot script to generate pdos.eps
20) README : this file
To run this example, simply invoke:
-> lmp -in in.EAM3D -screen none
Once done, one can use the auxiliary analysing code "phana" to obtain "disp.dat" and
"dos.dat" based on data from CuPhonon.bin.6500000:
-> phana CuPhonon.bin.6500000 < in.disp
-> phana CuPhonon.bin.6500000 < in.dos
And then use the gnuplot script file "plot.disp"/"plot.dos" to generate pdisp.eps/pdos.eps:
-> gnuplot plot.pdisp
-> gnuplot plot.pdos
The resultant ``pdisp.eps/pdos.eps'' compares the measured phonon dispersion to
experimental data and those by traditional lattice dynamics.
NOTE: the binary file provided here might be unreadable on some computers because of
incompatibility between different architectures.
Author: Ling-Ti Kong, konglt@sjtu.edu.cn
Feb 2013

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Cu functions (universal 3)
29 63.550 3.6150 FCC
500 5.0100200400801306e-04 500 1.0000000000000009e-02 4.9499999999999886e+00
0. -3.1561636903424350e-01 -5.2324876182494506e-01 -6.9740831416804383e-01 -8.5202525457518519e-01
-9.9329216586042435e-01 -1.1246331970890324e+00 -1.2481882647347859e+00 -1.3654054700363645e+00 -1.4773214276236644e+00
-1.5847099936904741e+00 -1.6865851873526410e+00 -1.7843534091637920e+00 -1.8790616476576076e+00 -1.9710188604521761e+00
-2.0604838665854572e+00 -2.1476762477372944e+00 -2.2327843595560068e+00 -2.3159713409697673e+00 -2.3973797031286352e+00
-2.4771348895887826e+00 -2.5553480773272810e+00 -2.6321184083774227e+00 -2.7075347880408458e+00 -2.7816773487592030e+00
-2.8546186529652005e+00 -2.9264246898861899e+00 -2.9971557080624507e+00 -3.0668669157065978e+00 -3.1356090736776849e+00
-3.2034290008357829e+00 -3.2703700069757247e+00 -3.3364722658277230e+00 -3.4017731379735778e+00 -3.4663074517059016e+00
-3.5301077484029122e+00 -3.5932044977085980e+00 -3.6556262870729199e+00 -3.7173999892229403e+00 -3.7785509106421671e+00
-3.8391029237823773e+00 -3.8990785849196925e+00 -3.9584992397079333e+00 -4.0173851179270912e+00 -4.0744518500210916e+00
-4.1306733564032641e+00 -4.1864034067843932e+00 -4.2416582335814326e+00 -4.2964533268445280e+00 -4.3508034838872618e+00
-4.4047228547107977e+00 -4.4582249835318351e+00 -4.5113228468570128e+00 -4.5640288884490872e+00 -4.6163550514904443e+00
-4.6683128082199232e+00 -4.7199131872767452e+00 -4.7711667990036801e+00 -4.8220838587683374e+00 -4.8726742087289665e+00
-4.9229473379113813e+00 -4.9729124009208192e+00 -5.0225782353423369e+00 -5.0719533779533492e+00 -5.1210460798461668e+00
-5.1698643205481289e+00 -5.2184158212228908e+00 -5.2667080570261362e+00 -5.3147482686812282e+00 -5.3625434733324937e+00
-5.4101004747367369e+00 -5.4574258728391953e+00 -5.5045260727784751e+00 -5.5514072933650311e+00 -5.5980755750691458e+00
-5.6445367875538750e+00 -5.6907966367860183e+00 -5.7368606717507191e+00 -5.7827342908000219e+00 -5.8284227476608805e+00
-5.8739311571204382e+00 -5.9192645004390272e+00 -5.9644276303605182e+00 -6.0094252761103064e+00 -6.0542620478988169e+00
-6.0989424413057520e+00 -6.1434708414539330e+00 -6.1878515269578429e+00 -6.2320886736884802e+00 -6.2761863583589275e+00
-6.3201485619430571e+00 -6.3639791729330000e+00 -6.4076819904493902e+00 -6.4512607272098990e+00 -6.4947190123648113e+00
-6.5380603942065250e+00 -6.5812883427622069e+00 -6.6243939095620874e+00 -6.6670830925929181e+00 -6.7096660473058591e+00
-6.7521459135001862e+00 -6.7945257643836499e+00 -6.8368086085521611e+00 -6.8789973918942735e+00 -6.9210949994162263e+00
-6.9631042569970703e+00 -7.0050279330721992e+00 -7.0468687402560874e+00 -7.0886293368973554e+00 -7.1303123285804020e+00
-7.1719202695651916e+00 -7.2134556641788095e+00 -7.2549209681507421e+00 -7.2963185899023415e+00 -7.3376508917899628e+00
-7.3789201913012903e+00 -7.4201287622117036e+00 -7.4612788356982946e+00 -7.5023726014152032e+00 -7.5434122085331978e+00
-7.5843997667427345e+00 -7.6253373472216595e+00 -7.6662269835740062e+00 -7.7070706727342895e+00 -7.7478703758424388e+00
-7.7886280190928119e+00 -7.8293454945503811e+00 -7.8700246609474789e+00 -7.9106673444489104e+00 -7.9512753393968865e+00
-7.9918504090315139e+00 -8.0323942861870705e+00 -8.0729086739704030e+00 -8.1133952464140293e+00 -8.1538556491162808e+00
-8.1942914998523975e+00 -8.2347043891773524e+00 -8.2750958810033808e+00 -8.3154675131659701e+00 -8.3558207979692725e+00
-8.3961572227176475e+00 -8.4364782502312892e+00 -8.4767853193496308e+00 -8.5170798454139458e+00 -8.5573632207473906e+00
-8.5976368151087286e+00 -8.6379019761436666e+00 -8.6781600298199919e+00 -8.7184122808490656e+00 -8.7586600130993020e+00
-8.7989044899963460e+00 -8.8391469549140993e+00 -8.8793886315543773e+00 -8.9196307243150841e+00 -8.9598744186541239e+00
-9.0001208814363167e+00 -9.0403712612778122e+00 -9.0806266888772029e+00 -9.1208882773446476e+00 -9.1611571225108719e+00
-9.2014343032440138e+00 -9.2417208817437881e+00 -9.2820179038447463e+00 -9.3223263992829857e+00 -9.3626473819958278e+00
-9.4029818503831279e+00 -9.4433307875392529e+00 -9.4836951616705960e+00 -9.5237840547885071e+00 -9.5637918926951784e+00
-9.6038142178817338e+00 -9.6438519061474608e+00 -9.6839058194810832e+00 -9.7239768064614509e+00 -9.7640657024289226e+00
-9.8041733297054634e+00 -9.8443004978059889e+00 -9.8844480036373170e+00 -9.9246166317080906e+00 -9.9648071543198853e+00
-1.0005020331762637e+01 -1.0045256912501884e+01 -1.0085517633366123e+01 -1.0125803219723423e+01 -1.0166114385662183e+01
-1.0206451834160134e+01 -1.0246816257258331e+01 -1.0287208336224353e+01 -1.0327628741713852e+01 -1.0368078133934148e+01
-1.0408557162795717e+01 -1.0449066468066974e+01 -1.0489606679525650e+01 -1.0530178417100558e+01 -1.0570782291022510e+01
-1.0611418901960292e+01 -1.0652088841158786e+01 -1.0692792690577562e+01 -1.0733531023022920e+01 -1.0774304402276016e+01
-1.0815113383222808e+01 -1.0855958511980305e+01 -1.0896840326017184e+01 -1.0937759354276295e+01 -1.0978716117290730e+01
-1.1019711127305925e+01 -1.1060744888386239e+01 -1.1101817896531486e+01 -1.1142930639787664e+01 -1.1184083598352004e+01
-1.1225277244679319e+01 -1.1266512043589387e+01 -1.1307788452364719e+01 -1.1349106920870327e+01 -1.1390467891550486e+01
-1.1431871799781504e+01 -1.1473319073642074e+01 -1.1514810134213008e+01 -1.1556345395619132e+01 -1.1597925265115521e+01
-1.1639550143177303e+01 -1.1681220423591583e+01 -1.1722936493536452e+01 -1.1764698733669888e+01 -1.1806507518187232e+01
-1.1848363215029394e+01 -1.1890266185706139e+01 -1.1932216785634637e+01 -1.1974215364086319e+01 -1.2016262264291129e+01
-1.2058357823507606e+01 -1.2100502373105996e+01 -1.2142696238631970e+01 -1.2184939739884385e+01 -1.2227233190982815e+01
-1.2269576900438324e+01 -1.2311971171220080e+01 -1.2354416300827552e+01 -1.2396912581348374e+01 -1.2439460299532641e+01
-1.2482059736851909e+01 -1.2524711169562636e+01 -1.2567414868772744e+01 -1.2610171100495961e+01 -1.2652980125719694e+01
-1.2695842200459083e+01 -1.2738757575819193e+01 -1.2781726498053729e+01 -1.2824749208615117e+01 -1.2867825944219817e+01
-1.2910956936899197e+01 -1.2954142414054047e+01 -1.2997382598508125e+01 -1.3040677708563408e+01 -1.3084027958052218e+01
-1.3127433556386677e+01 -1.3170894708610035e+01 -1.3214411615448739e+01 -1.3257984473359954e+01 -1.3301613474583519e+01
-1.3345298807190659e+01 -1.3389040655121903e+01 -1.3432839198243016e+01 -1.3476694612386723e+01 -1.3520607069407617e+01
-1.3564576737214225e+01 -1.3608603779754390e+01 -1.3652688357330362e+01 -1.3696830626228689e+01 -1.3741030739041094e+01
-1.3785288844633044e+01 -1.3829605088192579e+01 -1.3873979611263849e+01 -1.3918412551792358e+01 -1.3962904044165157e+01
-1.4007454219246995e+01 -1.4052063204422609e+01 -1.4096731123636516e+01 -1.4141458097424390e+01 -1.4186244242962175e+01
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524
examples/USER/phonon/3-3D-FCC-Cu-EAM/data.pos Normal file
View File

@ -0,0 +1,524 @@
FCC(001) cell with dimension 8 x 8 x 8
512 atoms
1 atom types
0.00000000 20.44952811 xlo xhi
0.00000000 17.70981084 ylo yhi
0.00000000 16.69696978 zlo zhi
10.22476405 10.22476405 5.90327028 xy xz yz
Atoms
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464 1 28.11810115 7.37908785 14.60984856
465 1 11.50285956 9.59281421 14.60984856
466 1 14.05905058 9.59281421 14.60984856
467 1 16.61524159 9.59281421 14.60984856
468 1 19.17143260 9.59281421 14.60984856
469 1 21.72762362 9.59281421 14.60984856
470 1 24.28381463 9.59281421 14.60984856
471 1 26.84000565 9.59281421 14.60984856
472 1 29.39619666 9.59281421 14.60984856
473 1 12.78095507 11.80654056 14.60984856
474 1 15.33714608 11.80654056 14.60984856
475 1 17.89333710 11.80654056 14.60984856
476 1 20.44952811 11.80654056 14.60984856
477 1 23.00571913 11.80654056 14.60984856
478 1 25.56191014 11.80654056 14.60984856
479 1 28.11810115 11.80654056 14.60984856
480 1 30.67429217 11.80654056 14.60984856
481 1 14.05905058 14.02026692 14.60984856
482 1 16.61524159 14.02026692 14.60984856
483 1 19.17143260 14.02026692 14.60984856
484 1 21.72762362 14.02026692 14.60984856
485 1 24.28381463 14.02026692 14.60984856
486 1 26.84000565 14.02026692 14.60984856
487 1 29.39619666 14.02026692 14.60984856
488 1 31.95238767 14.02026692 14.60984856
489 1 15.33714608 16.23399327 14.60984856
490 1 17.89333710 16.23399327 14.60984856
491 1 20.44952811 16.23399327 14.60984856
492 1 23.00571913 16.23399327 14.60984856
493 1 25.56191014 16.23399327 14.60984856
494 1 28.11810115 16.23399327 14.60984856
495 1 30.67429217 16.23399327 14.60984856
496 1 33.23048318 16.23399327 14.60984856
497 1 16.61524159 18.44771963 14.60984856
498 1 19.17143260 18.44771963 14.60984856
499 1 21.72762362 18.44771963 14.60984856
500 1 24.28381463 18.44771963 14.60984856
501 1 26.84000565 18.44771963 14.60984856
502 1 29.39619666 18.44771963 14.60984856
503 1 31.95238767 18.44771963 14.60984856
504 1 34.50857869 18.44771963 14.60984856
505 1 17.89333710 20.66144598 14.60984856
506 1 20.44952811 20.66144598 14.60984856
507 1 23.00571913 20.66144598 14.60984856
508 1 25.56191014 20.66144598 14.60984856
509 1 28.11810115 20.66144598 14.60984856
510 1 30.67429217 20.66144598 14.60984856
511 1 33.23048318 20.66144598 14.60984856
512 1 35.78667420 20.66144598 14.60984856

83
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat Normal file
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#phonon dispersion for Cu at 298K
# from Phys Rev 164, 922 (1967).
# x v_298 v_49 dv qr
#
#00x from G (0,0,0) to X (0.5, 0, 0.5)
0.20 2.440 2.43 0.040 0.141421
0.30 3.560 3.56 0.040 0.212132
0.40 4.500 4.56 0.050 0.282843
0.50 5.420 5.44 0.070 0.353553
0.60 6.140 6.15 0.100 0.424264
0.70 6.660 6.66 0.100 0.494975
0.80 6.900 6.90 0.150 0.565685
0.90 7.150 7.18 0.170 0.636396
1.00 7.200 7.25 0.200 0.707107
#00x
0.20 1.600 1.65 0.020 0.141421
0.30 2.350 2.40 0.020 0.212132
0.40 3.050 3.09 0.020 0.282843
0.50 3.670 3.69 0.030 0.353553
0.60 4.170 4.22 0.030 0.424264
0.70 4.590 4.64 0.000 0.494975
0.80 4.880 4.94 0.100 0.565685
0.90 5.070 5.08 0.100 0.636396
1.00 5.090 5.13 0.150 0.707107
#xx0 from (0.5,1.0,0.5) to (0,0,0)
0.10 1.960 2.01 0.02 2.51648
0.20 3.670 3.73 0.03 2.39401
0.30 5.030 5.1O 0.07 2.27153
0.40 6.000 6.05 0.10 2.14906
0.50 6.350 6.42 0.15 2.02659
0.60 6.350 6.39 0.15 1.90411
0.70 6.140 6.18 0.10 1.78164
0.80 5.710 5.80 0.15 1.65916
1.00 5.090 5.13 0.15 1.41421
#xx0
0.10 1.120 1.21 0.015 2.51648
0.20 2.345 2.385 0.020 2.39401
0.30 3.410 3.46 0.030 2.27153
0.40 4.330 4.39 0.030 2.14906
0.50 5.120 5.16 0.060 2.02659
0.60 5.760 5.85 0.070 1.90411
0.70 6.390 6.40 0.120 1.78164
0.80 6.790 6.84 0.150 1.65916
0.90 7.080 7.05 0.200 1.53669
1.00 7.200 7.25 0.200 1.41421
#xx0
0.25 1.730 1.79 0.03 2.33277
0.30 2.070 2.12 0.04 2.27153
0.40 2.730 2.79 0.03 2.14906
0.50 3.390 3.43 0.04 2.02659
0.60 3.850 3.93 0.07 1.90411
0.70 4.330 4.40 0.00 1.78164
0.80 4.700 4.80 0.06 1.65916
0.90 4.930 5.07 0.10 1.53669
1.00 5.090 5.13 0.15 1.41421
#xxx from (0,0,0) to (0.5, 0.5, 0.5)
0.05 1.220 1.22 0.03 2.72556
0.10 2.490 2.49 0.05 2.81216
0.15 3.590 3.59 0.00 2.89877
0.20 4.570 4.61 0.05 2.98537
0.25 5.460 5.51 0.10 3.07197
0.30 6.180 6.21 0.10 3.15857
0.35 6.710 6.80 0.15 3.24518
0.40 7.010 7.12 0.15 3.33178
0.45 7.160 7.27 0.20 3.41838
0.50 7.290 7.30 0.20 3.50498
#xxx
0.10 0.980 1.05 0.06 2.81216
0.15 1.440 1.53 0.06 2.89877
0.20 1.890 1.90 0.06 2.98537
0.25 2.300 2.35 0.04 3.07197
0.30 2.690 2.72 0.05 3.15857
0.35 2.980 3.03 0.06 3.24518
0.40 3.210 3.24 0.07 3.33178
0.45 3.370 3.39 0.08 3.41838
0.50 3.410 3.42 0.10 3.50498
#10x from (0.5,0,0.5) via (0.5, 0.25, 0.75) then back to ( 0.5, 0., 0.5)
0.50 4.890 4.95 0.09 1.06066
0.60 4.970 4.96 0.09 1.13137
0.70 5.000 4.98 0.10 1.20208
0.80 5.020 5.08 0.10 1.27279
0.90 5.050 5.11 0.10 1.3435
1.00 5.090 5.13 0.15 1.41421

86
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat Normal file
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# index qr qx qy qz 3-frequencies
1 0 0 0 0 0 0 0
2 0.0294628 0.0208333 0 0.0208333 0.347321 0.347321 0.439772
3 0.0589256 0.0416667 0 0.0416667 0.69303 0.69303 0.879729
4 0.0883883 0.0625 0 0.0625 1.03553 1.03553 1.31996
5 0.117851 0.0833333 0 0.0833333 1.37323 1.37323 1.76037
6 0.147314 0.104167 0 0.104167 1.70461 1.70461 2.20059
7 0.176777 0.125 0 0.125 2.02815 2.02815 2.63994
8 0.206239 0.145833 0 0.145833 2.34242 2.34242 3.07736
9 0.235702 0.166667 0 0.166667 2.64603 2.64603 3.51142
10 0.265165 0.1875 0 0.1875 2.93767 2.93767 3.94028
11 0.294628 0.208333 0 0.208333 3.21609 3.21609 4.36173
12 0.324091 0.229167 0 0.229167 3.48015 3.48015 4.77325
13 0.353553 0.25 0 0.25 3.72877 3.72877 5.17202
14 0.383016 0.270833 0 0.270833 3.96096 3.96096 5.555
15 0.412479 0.291667 0 0.291667 4.17583 4.17583 5.91902
16 0.441942 0.3125 0 0.3125 4.37257 4.37257 6.26082
17 0.471405 0.333333 0 0.333333 4.55046 4.55046 6.57717
18 0.500867 0.354167 0 0.354167 4.70886 4.70886 6.86491
19 0.53033 0.375 0 0.375 4.84722 4.84722 7.12106
20 0.559793 0.395833 0 0.395833 4.96506 4.96506 7.34288
21 0.589256 0.416667 0 0.416667 5.06201 5.06201 7.52792
22 0.618718 0.4375 0 0.4375 5.13773 5.13773 7.67409
23 0.648181 0.458333 0 0.458333 5.19199 5.19199 7.77973
24 0.677644 0.479167 0 0.479167 5.22461 5.22461 7.84362
25 0.707107 0.5 0 0.5 5.2355 5.2355 7.86499
26 0.707107 0.5 0 0.5 5.2355 5.2355 7.86499
27 0.795495 0.5 0.0625 0.5625 5.22438 5.36797 7.78721
28 0.883883 0.5 0.125 0.625 5.19745 5.72491 7.55862
29 0.972272 0.5 0.1875 0.6875 5.17037 6.21195 7.19519
30 1.06066 0.5 0.25 0.75 5.15912 6.72853 6.72853
31 1.06066 0.5 0.25 0.75 5.15912 6.72853 6.72853
32 1.14905 0.5 0.1875 0.6875 5.17037 6.21195 7.19519
33 1.23744 0.5 0.125 0.625 5.19745 5.72491 7.55862
34 1.32583 0.5 0.0625 0.5625 5.22438 5.36797 7.78721
35 1.41421 0.5 0 0.5 5.2355 5.2355 7.86499
36 1.41421 0.5 1 0.5 5.2355 5.2355 7.86499
37 1.46524 0.479167 0.958333 0.479167 5.21956 5.2786 7.84763
38 1.51628 0.458333 0.916667 0.458333 5.172 5.40182 7.79557
39 1.56731 0.4375 0.875 0.4375 5.09349 5.58857 7.70898
40 1.61834 0.416667 0.833333 0.416667 4.98517 5.81577 7.5881
41 1.66937 0.395833 0.791667 0.395833 4.8486 6.0582 7.43334
42 1.7204 0.375 0.75 0.375 4.68568 6.29175 7.24527
43 1.77143 0.354167 0.708333 0.354167 4.49867 6.49527 7.02466
44 1.82246 0.333333 0.666667 0.333333 4.29007 6.65135 6.77253
45 1.87349 0.3125 0.625 0.3125 4.06259 6.49014 6.74643
46 1.92452 0.291667 0.583333 0.291667 3.81906 6.17901 6.77065
47 1.97555 0.270833 0.541667 0.270833 3.56237 5.84092 6.71753
48 2.02659 0.25 0.5 0.25 3.29539 5.47787 6.58361
49 2.07762 0.229167 0.458333 0.229167 3.02087 5.09207 6.36811
50 2.12865 0.208333 0.416667 0.208333 2.74139 4.68588 6.07251
51 2.17968 0.1875 0.375 0.1875 2.45928 4.26171 5.70023
52 2.23071 0.166667 0.333333 0.166667 2.17654 3.82203 5.25624
53 2.28174 0.145833 0.291667 0.145833 1.89481 3.36921 4.74676
54 2.33277 0.125 0.25 0.125 1.6153 2.90555 4.17889
55 2.3838 0.104167 0.208333 0.104167 1.33881 2.43315 3.56039
56 2.43483 0.0833333 0.166667 0.0833333 1.06568 1.95394 2.89942
57 2.48587 0.0625 0.125 0.0625 0.795832 1.4696 2.20438
58 2.5369 0.0416667 0.0833333 0.0416667 0.528811 0.981646 1.48378
59 2.58793 0.0208333 0.0416667 0.0208333 0.26386 0.491382 0.746146
60 2.63896 0 0 0 0 0 0
61 2.63896 0 0 0 0 0 0
62 2.67504 0.0208333 0.0208333 0.0208333 0.217972 0.217972 0.480503
63 2.71113 0.0416667 0.0416667 0.0416667 0.434931 0.434931 0.959746
64 2.74721 0.0625 0.0625 0.0625 0.649869 0.649869 1.43644
65 2.7833 0.0833333 0.0833333 0.0833333 0.861796 0.861796 1.90925
66 2.81938 0.104167 0.104167 0.104167 1.06974 1.06974 2.37675
67 2.85546 0.125 0.125 0.125 1.27276 1.27276 2.83745
68 2.89155 0.145833 0.145833 0.145833 1.46995 1.46995 3.2897
69 2.92763 0.166667 0.166667 0.166667 1.66044 1.66044 3.7318
70 2.96372 0.1875 0.1875 0.1875 1.84341 1.84341 4.1619
71 2.9998 0.208333 0.208333 0.208333 2.01808 2.01808 4.57805
72 3.03589 0.229167 0.229167 0.229167 2.18372 2.18372 4.97822
73 3.07197 0.25 0.25 0.25 2.33966 2.33966 5.36031
74 3.10806 0.270833 0.270833 0.270833 2.48529 2.48529 5.72215
75 3.14414 0.291667 0.291667 0.291667 2.62004 2.62004 6.0616
76 3.18022 0.3125 0.3125 0.3125 2.74342 2.74342 6.37651
77 3.21631 0.333333 0.333333 0.333333 2.85496 2.85496 6.6648
78 3.25239 0.354167 0.354167 0.354167 2.95427 2.95427 6.92447
79 3.28848 0.375 0.375 0.375 3.04102 3.04102 7.15367
80 3.32456 0.395833 0.395833 0.395833 3.1149 3.1149 7.3507
81 3.36065 0.416667 0.416667 0.416667 3.17567 3.17567 7.51406
82 3.39673 0.4375 0.4375 0.4375 3.22314 3.22314 7.64248
83 3.43282 0.458333 0.458333 0.458333 3.25715 3.25715 7.73495
84 3.4689 0.479167 0.479167 0.479167 3.2776 3.2776 7.79074
85 3.50498 0.5 0.5 0.5 3.28442 3.28442 7.80938

47
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat Normal file
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# q qr freq
# 2pi/L 2pi/L THz
0 0 0 0 0 0 0
0.0555556 0 0.0555556 0.0785674 0.911142 1.09803 1.39027
0.111111 0 0.111111 0.157135 1.72052 1.74787 2.59975
0.166667 0 0.166667 0.235702 2.44336 2.50586 3.63408
0.222222 0 0.222222 0.31427 3.15319 3.23021 4.63176
0.277778 0 0.277778 0.392837 3.7348 3.80727 5.52493
0.333333 0 0.333333 0.471405 4.14632 4.24267 6.31106
0.388889 0 0.388889 0.549972 4.43331 4.54654 6.83324
0.444444 0 0.444444 0.628539 4.80057 4.91768 7.2618
0.5 0 0.5 0.707107 4.99873 5.05094 7.49212
0.5 0 0.5 0.707107 4.99873 5.05094 7.49212
0.5 0.0625 0.5625 0.795495 4.92887 5.10253 7.33029
0.5 0.125 0.625 0.883883 4.8516 5.45554 7.19429
0.5 0.1875 0.6875 0.972272 4.84544 5.82933 6.77906
0.5 0.25 0.75 1.06066 4.79502 6.26993 6.39208
0.5 0.25 0.75 1.06066 4.79502 6.26993 6.39208
0.5 0.1875 0.6875 1.14905 4.84544 5.82933 6.77906
0.5 0.125 0.625 1.23744 4.8516 5.45554 7.19429
0.5 0.0625 0.5625 1.32583 4.92887 5.10253 7.33029
0.5 0 0.5 1.41421 4.99873 5.05094 7.49212
0.5 1 0.5 1.41421 4.99873 5.05094 7.49212
0.464286 0.928571 0.464286 1.5017 4.94306 5.02929 7.33752
0.428571 0.857143 0.428571 1.58918 4.73096 5.28746 7.22892
0.392857 0.785714 0.392857 1.67666 4.41656 5.67558 6.97967
0.357143 0.714286 0.357143 1.76414 4.12241 6.03251 6.61209
0.321429 0.642857 0.321429 1.85162 3.85271 6.14006 6.34226
0.285714 0.571429 0.285714 1.9391 3.4839 5.63477 6.43155
0.25 0.5 0.25 2.02659 2.97818 5.0339 6.42743
0.214286 0.428571 0.214286 2.11407 2.58695 4.4395 6.018
0.178571 0.357143 0.178571 2.20155 2.17788 3.76189 5.42678
0.142857 0.285714 0.142857 2.28903 1.65866 3.07149 4.66586
0.107143 0.214286 0.107143 2.37651 1.23216 2.39432 3.81551
0.0714286 0.142857 0.0714286 2.46399 0.877558 1.59175 2.56147
0.0357143 0.0714286 0.0357143 2.55148 0.61088 0.898697 1.33765
1.66533e-16 3.33067e-16 1.66533e-16 2.63896 -1.09674e-08 4.6235e-15 1.09674e-08
0 0 0 2.63896 0 0 0
0.0555556 0.0555556 0.0555556 2.73518 0.756899 0.831031 1.38038
0.111111 0.111111 0.111111 2.83141 1.04303 1.08638 2.64368
0.166667 0.166667 0.166667 2.92763 1.63834 1.64672 3.80587
0.222222 0.222222 0.222222 3.02386 1.97746 2.01688 4.85974
0.277778 0.277778 0.277778 3.12008 2.30453 2.36696 5.68513
0.333333 0.333333 0.333333 3.21631 2.65806 2.7654 6.4126
0.388889 0.388889 0.388889 3.31253 2.8655 2.97378 6.94257
0.444444 0.444444 0.444444 3.40876 3.01201 3.11788 7.32217
0.5 0.5 0.5 3.50498 2.95362 3.11441 7.53349

164
examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat Normal file
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# PDOS of Copper at 298 K
# Phys Rev 164, 922 (1967)
1.56e-05 0
0.135081 0
0.176624 0
0.342828 0.00136913
0.498642 0.00268108
0.602476 0.00355536
0.685609 0.0043255
0.846586 0.0058168
0.893293 0.0062495
0.966005 0.00756643
1.16845 0.011233
1.16849 0.0112341
1.3346 0.0149823
1.49028 0.0184952
1.51628 0.0193117
1.65121 0.023548
1.82764 0.0290878
1.83795 0.0294116
2.00924 0.0363333
2.16478 0.0426182
2.16487 0.0426233
2.19837 0.044404
2.28419 0.0489662
2.38775 0.0544708
2.40344 0.0555066
2.48119 0.0606386
2.5849 0.067484
2.65727 0.0722606
2.65742 0.072273
2.74553 0.0792169
2.81801 0.0849288
2.85414 0.0877762
2.89571 0.092199
2.98889 0.102111
3.03012 0.106496
3.08722 0.114907
3.1492 0.124036
3.16968 0.127053
3.19567 0.133012
3.27821 0.151939
3.31916 0.161328
3.32972 0.167405
3.35535 0.182152
3.39619 0.205652
3.40576 0.211163
3.416 0.215734
3.4162 0.215743
3.4525 0.217337
3.55622 0.221892
3.57161 0.222568
3.76349 0.232139
3.95538 0.241252
3.97112 0.241997
4.15765 0.250822
4.27712 0.255917
4.52076 0.266309
4.55723 0.267772
4.70233 0.273595
4.80105 0.27687
4.89432 0.279965
4.91012 0.273559
4.91039 0.265784
4.9526 0.246569
4.95669 0.245298
4.96723 0.242016
4.978 0.238665
4.98351 0.236951
4.98936 0.23513
5.00986 0.230982
5.04667 0.223531
5.07305 0.218194
5.09904 0.214018
5.13574 0.208122
5.14099 0.207805
5.16213 0.20653
5.17791 0.205579
5.23464 0.202159
5.2714 0.200491
5.41674 0.193896
5.43771 0.192787
5.54685 0.187014
5.57811 0.183809
5.67196 0.174186
5.70825 0.169617
5.79196 0.159074
5.81762 0.153984
5.87041 0.143511
5.91157 0.133554
5.93851 0.127035
5.99619 0.111476
6.00561 0.107735
6.03305 0.0968351
6.07381 0.0851029
6.08552 0.081734
6.11661 0.0840154
6.12114 0.0851131
6.1683 0.0965218
6.17328 0.0977261
6.19356 0.112357
6.20465 0.118323
6.21906 0.126072
6.23551 0.135326
6.27513 0.157619
6.28117 0.160817
6.33125 0.187336
6.34205 0.196676
6.38226 0.231463
6.38675 0.235347
6.41686 0.266441
6.41712 0.267067
6.43609 0.311714
6.43642 0.312105
6.45106 0.329547
6.48165 0.346463
6.49783 0.35179
6.53302 0.363376
6.54883 0.368721
6.58438 0.380746
6.62041 0.394307
6.63053 0.398117
6.67676 0.413658
6.71769 0.422835
6.72301 0.427471
6.74978 0.432286
6.75437 0.431902
6.7556 0.432212
6.75904 0.437883
6.76896 0.451602
6.77181 0.368366
6.77242 0.350529
6.77414 0.347671
6.78061 0.336938
6.78344 0.332234
6.79445 0.313938
6.80243 0.307449
6.81382 0.298185
6.81583 0.296556
6.82681 0.279176
6.84107 0.268177
6.84815 0.262708
6.86435 0.244869
6.87361 0.238652
6.89093 0.227029
6.90577 0.218282
6.92274 0.208272
6.93259 0.203523
6.95972 0.19043
6.98014 0.180328
6.99671 0.17213
7.03292 0.15711
7.04413 0.152457
7.07066 0.136445
7.0859 0.12832
7.1024 0.119518
7.17116 0.0838345
7.1968 0.060699
7.20868 0.0499852
7.25556 0.0359078
7.25592 0.0357998
7.28826 0.0222715
7.31389 0.0115511
7.32466 0.000573158

101
examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat Normal file
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# nu DOS
0.040404 2.93333e-05
0.121212 0.000156444
0.20202 0.000234667
0.282828 0.00088
0.363636 0.001056
0.444444 0.00179911
0.525253 0.00291378
0.606061 0.00348089
0.686869 0.00391111
0.767677 0.005632
0.848485 0.00561244
0.929293 0.008448
1.0101 0.00973867
1.09091 0.0101884
1.17172 0.0127893
1.25253 0.0149013
1.33333 0.0149404
1.41414 0.0194187
1.49495 0.0219413
1.57576 0.0215111
1.65657 0.02728
1.73737 0.0290204
1.81818 0.028864
1.89899 0.037664
1.9798 0.0355324
2.06061 0.0420444
2.14141 0.0466987
2.22222 0.0479307
2.30303 0.0548338
2.38384 0.0589404
2.46465 0.0652373
2.54545 0.0690898
2.62626 0.0741938
2.70707 0.0810773
2.78788 0.0897404
2.86869 0.0975431
2.94949 0.102628
3.0303 0.117568
3.11111 0.129908
3.19192 0.142443
3.27273 0.173301
3.35354 0.192955
3.43434 0.185973
3.51515 0.199115
3.59596 0.196729
3.67677 0.2068
3.75758 0.2024
3.83838 0.20858
3.91919 0.210789
4 0.210027
4.08081 0.217419
4.16162 0.214857
4.24242 0.230795
4.32323 0.225515
4.40404 0.225476
4.48485 0.231792
4.56566 0.231381
4.64646 0.236857
4.72727 0.23848
4.80808 0.240885
4.88889 0.249294
4.9697 0.242704
5.05051 0.259541
5.13131 0.247886
5.21212 0.176763
5.29293 0.149717
5.37374 0.15003
5.45455 0.156229
5.53535 0.144085
5.61616 0.15402
5.69697 0.149541
5.77778 0.148192
5.85859 0.149678
5.93939 0.149893
6.0202 0.146901
6.10101 0.14475
6.18182 0.153296
6.26263 0.139588
6.34343 0.135109
6.42424 0.135403
6.50505 0.131609
6.58586 0.115867
6.66667 0.109433
6.74747 0.143792
6.82828 0.192036
6.90909 0.220293
6.9899 0.257038
7.07071 0.273093
7.15152 0.311246
7.23232 0.337705
7.31313 0.291808
7.39394 0.222132
7.47475 0.183529
7.55556 0.151145
7.63636 0.118761
7.71717 0.0815271
7.79798 0.0323058
7.87879 0.00111467
7.9596 0
8.0404 0

102
examples/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat Normal file
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# frequency DOS
#THz number
0.0375 0.000106667
0.1125 0
0.1875 0.000426667
0.2625 0.000213333
0.3375 0.000213333
0.4125 0.00163556
0.4875 0.00163556
0.5625 0.00206222
0.6375 0.00256
0.7125 0.00348444
0.7875 0.00483556
0.8625 0.00704
0.9375 0.00945778
1.0125 0.0103822
1.0875 0.0137244
1.1625 0.0140089
1.2375 0.0184889
1.3125 0.0178489
1.3875 0.0243911
1.4625 0.0233244
1.5375 0.0264533
1.6125 0.0302933
1.6875 0.0323556
1.7625 0.0359822
1.8375 0.0397511
1.9125 0.0412444
1.9875 0.0511289
2.0625 0.0514844
2.1375 0.0559644
2.2125 0.0649956
2.2875 0.0666311
2.3625 0.0734578
2.4375 0.0812089
2.5125 0.08448
2.5875 0.0991289
2.6625 0.0979911
2.7375 0.111289
2.8125 0.124089
2.8875 0.13376
2.9625 0.160036
3.0375 0.181796
3.1125 0.188373
3.1875 0.211911
3.2625 0.212836
3.3375 0.205653
3.4125 0.212196
3.4875 0.2208
3.5625 0.219164
3.6375 0.228124
3.7125 0.222933
3.7875 0.232036
3.8625 0.234809
3.9375 0.234098
4.0125 0.242133
4.0875 0.237582
4.1625 0.242631
4.2375 0.251093
4.3125 0.245049
4.3875 0.253511
4.4625 0.251662
4.5375 0.254933
4.6125 0.257991
4.6875 0.253653
4.7625 0.251947
4.8375 0.197156
4.9125 0.166258
4.9875 0.162311
5.0625 0.159218
5.1375 0.156373
5.2125 0.160996
5.2875 0.152107
5.3625 0.160213
5.4375 0.151253
5.5125 0.155449
5.5875 0.1536
5.6625 0.152178
5.7375 0.152249
5.8125 0.14848
5.8875 0.146702
5.9625 0.141298
6.0375 0.13312
6.1125 0.123662
6.1875 0.115698
6.2625 0.112142
6.3375 0.160142
6.4125 0.21696
6.4875 0.250098
6.5625 0.273209
6.6375 0.306489
6.7125 0.337493
6.7875 0.363804
6.8625 0.329884
6.9375 0.253582
7.0125 0.207431
7.0875 0.173724
7.1625 0.144142
7.2375 0.111253
7.3125 0.0369422
7.3875 0.00323556
7.4625 0

40
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D Normal file
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# 3D copper block simulation
boundary p p p
units metal
atom_style atomic
# geometry
read_data data.pos
# EAM potential
pair_style eam/opt
pair_coeff * * cuu3.eam
neighbor 0.5 nsq
neigh_modify every 1 delay 0 check yes
#Langevin random seed
variable r equal 57085
variable t equal 300
variable d equal 1
# initialize
velocity all create $t 28459 rot yes dist gaussian mom yes
reset_timestep 0
# fixes
fix 1 all npt temp $t $t $d iso 1. 1. 1. pchain 8 drag 1.0
fix 2 all phonon 10 50000 500000 map.in CuPhonon
#
timestep 2e-3
# output
# 1 2 3 4 5 6 7 8 9 10 11 12
thermo_style custom step temp pe ke press vol lx ly lz xy xz yz
thermo 100
restart 2000000 restart.one restart.two
# execution
run 6500000
write_restart Restart.final

21
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp Normal file
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1
1
2
disp.dat
0 0 0 ! Gamma
0.5 0 0.5 ! X
10
0.5 0 0.5 ! X
0.5 0.25 0.75 ! W
5
0.5 0.25 0.75 ! W
0.5 0 0.5 ! X
5
0.5 1. 0.5 ! X'
0 0 0 ! Gamma
15
0 0 0 ! Gamma
0.5 0.5 0.5 ! L
10
q
0

11
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.dos Normal file
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1
1
1
80 80 80
2
y
0 7.5
100
n
dosnew.dat
0

107
examples/USER/phonon/3-3D-FCC-Cu-EAM/log.lammps.example Normal file
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LAMMPS (21 Feb 2013)
# 3D copper block simulation
boundary p p p
units metal
atom_style atomic
# geometry
read_data data.pos
triclinic box = (0 0 0) to (20.4495 17.7098 16.697) with tilt (10.2248 10.2248 5.90327)
2 by 1 by 1 MPI processor grid
512 atoms
# EAM potential
pair_style eam/opt
pair_coeff * * cuu3.eam
neighbor 0.5 nsq
neigh_modify every 1 delay 0 check yes
#Langevin random seed
variable r equal 57085
variable t equal 300
variable d equal 1
# initialize
velocity all create $t 28459 rot yes dist gaussian mom yes
velocity all create 300 28459 rot yes dist gaussian mom yes
reset_timestep 0
# fixes
fix 1 all npt temp $t $t $d iso 1. 1. 1. pchain 8 drag 1.0
fix 1 all npt temp 300 $t $d iso 1. 1. 1. pchain 8 drag 1.0
fix 1 all npt temp 300 300 $d iso 1. 1. 1. pchain 8 drag 1.0
fix 1 all npt temp 300 300 1 iso 1. 1. 1. pchain 8 drag 1.0
fix 2 all phonon 10 50000 500000 map.in CuPhonon
#
timestep 2e-3
# output
# 1 2 3 4 5 6 7 8 9 10 11 12
thermo_style custom step temp pe ke press vol lx ly lz xy xz yz
thermo 100
restart 2000000 restart.one restart.two
# execution
run 6500000
Memory usage per processor = 1.99284 Mbytes
Step Temp PotEng KinEng Press Volume Lx Ly Lz Xy Xz Yz
0 300 -1812.48 19.81558 3500.1579 6046.9291 20.449528 17.709811 16.69697 10.224764 10.224764 5.9032703
100 153.63803 -1802.7325 10.148089 9969.8877 6046.1053 20.448599 17.709007 16.696212 10.2243 10.2243 5.9030022
200 147.66123 -1802.0353 9.7533097 6181.6515 6065.3651 20.470289 17.727791 16.713921 10.235145 10.235145 5.9092635
300 159.44388 -1802.4447 10.531577 1302.3641 6085.5588 20.492982 17.747443 16.73245 10.246491 10.246491 5.9158143
400 153.00479 -1801.6578 10.106262 -1272.5545 6099.3441 20.508444 17.760833 16.745074 10.254222 10.254222 5.9202778
500 161.86187 -1801.842 10.69129 -3430.236 6109.3399 20.519641 17.770531 16.754217 10.259821 10.259821 5.9235102
600 153.59685 -1800.8779 10.145369 -2860.2245 6109.8157 20.520174 17.770992 16.754652 10.260087 10.260087 5.923664
700 160.07641 -1800.8861 10.573356 -2239.7816 6107.275 20.517329 17.768528 16.752329 10.258665 10.258665 5.9228427
800 165.73442 -1800.8403 10.947079 -904.95606 6101.8375 20.511238 17.763253 16.747356 10.255619 10.255619 5.9210845
900 183.19989 -1801.5728 12.100707 -392.42323 6098.2511 20.507219 17.759773 16.744074 10.253609 10.253609 5.9199242
1000 162.15993 -1799.7547 10.710977 2745.7457 6089.0632 20.496915 17.750849 16.735661 10.248457 10.248457 5.9169496
...
6497500 307.52985 -1792.5473 20.312941 619.31021 6131.6172 20.544552 17.792104 16.774557 10.272276 10.272276 5.9307013
6497600 306.86159 -1792.5052 20.268801 -216.3856 6136.1966 20.549665 17.796532 16.778732 10.274833 10.274833 5.9321774
6497700 307.39996 -1792.5441 20.304362 -1228.3787 6140.5334 20.554505 17.800724 16.782683 10.277253 10.277253 5.9335746
6497800 293.9944 -1791.6597 19.418898 -450.0792 6139.4195 20.553263 17.799648 16.781669 10.276631 10.276631 5.9332158
6497900 313.02542 -1792.9199 20.675934 -1116.6261 6138.9447 20.552733 17.799189 16.781236 10.276366 10.276366 5.9330629
6498000 308.12517 -1792.5984 20.352264 19.870716 6135.0609 20.548397 17.795434 16.777696 10.274199 10.274199 5.9318114
6498100 297.5883 -1791.9056 19.656283 1183.6464 6131.2578 20.544151 17.791756 16.774229 10.272075 10.272075 5.9305855
6498200 318.62339 -1793.3014 21.045691 -558.41649 6134.9852 20.548313 17.795361 16.777627 10.274157 10.274157 5.931787
6498300 309.31473 -1792.6866 20.430836 -77.461979 6134.513 20.547786 17.794904 16.777197 10.273893 10.273893 5.9316348
6498400 302.20014 -1792.222 19.960903 723.61365 6132.0109 20.544992 17.792485 16.774916 10.272496 10.272496 5.9308283
6498500 300.44204 -1792.1064 19.844778 508.60679 6134.3039 20.547552 17.794702 16.777006 10.273776 10.273776 5.9315674
6498600 301.02636 -1792.1458 19.883374 -163.11994 6137.2413 20.550832 17.797542 16.779684 10.275416 10.275416 5.9325141
6498700 305.52569 -1792.4421 20.180563 -247.52326 6136.8028 20.550342 17.797118 16.779284 10.275171 10.275171 5.9323727
6498800 305.44716 -1792.4378 20.175375 -686.44372 6138.5481 20.55229 17.798805 16.780875 10.276145 10.276145 5.9329351
6498900 306.47904 -1792.5062 20.243533 -1558.472 6142.2496 20.55642 17.802382 16.784247 10.27821 10.27821 5.9341274
6499000 296.19916 -1791.8274 19.564527 -1327.6975 6142.7934 20.557027 17.802907 16.784742 10.278513 10.278513 5.9343025
6499100 297.83841 -1791.9367 19.672803 -1318.6973 6142.4329 20.556625 17.802559 16.784414 10.278312 10.278312 5.9341864
6499200 310.32619 -1792.7601 20.497645 -1248.6938 6140.2575 20.554198 17.800457 16.782432 10.277099 10.277099 5.9334858
6499300 303.00762 -1792.2744 20.014239 -455.90856 6138.2025 20.551904 17.798471 16.78056 10.275952 10.275952 5.9328238
6499400 298.93151 -1792.0026 19.745004 413.35674 6134.767 20.548069 17.79515 16.777428 10.274035 10.274035 5.9317167
6499500 297.91339 -1791.934 19.677755 1161.119 6131.5489 20.544476 17.792038 16.774494 10.272238 10.272238 5.9306793
6499600 302.8607 -1792.2598 20.004535 1575.6419 6128.6345 20.54122 17.789219 16.771836 10.27061 10.27061 5.9297395
6499700 293.31991 -1791.6317 19.374348 2344.8729 6126.6124 20.538961 17.787262 16.769991 10.26948 10.26948 5.9290873
6499800 307.59734 -1792.5808 20.317399 897.33724 6130.1931 20.542961 17.790726 16.773258 10.271481 10.271481 5.9302422
6499900 302.22243 -1792.2306 19.962376 633.39905 6133.3022 20.546434 17.793734 16.776093 10.273217 10.273217 5.9312446
6500000 311.80592 -1792.8634 20.595384 -794.36355 6137.8655 20.551528 17.798146 16.780252 10.275764 10.275764 5.9327152
Loop time of 3793.94 on 2 procs for 6500000 steps with 512 atoms
Pair time (%) = 2249.87 (59.3018)
Neigh time (%) = 1155.6 (30.4591)
Comm time (%) = 152.897 (4.03002)
Outpt time (%) = 3.23674 (0.0853134)
Other time (%) = 232.331 (6.12375)
Nlocal: 256 ave 259 max 253 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1265 ave 1268 max 1262 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 6923 ave 7073 max 6773 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 13846
Ave neighs/atom = 27.043
Neighbor list builds = 388421
Dangerous builds = 0
write_restart Restart.final

514
examples/USER/phonon/3-3D-FCC-Cu-EAM/map.in Normal file
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8 8 8 1
#l1 l2 l3 k atom_id
0 0 0 0 1
1 0 0 0 2
2 0 0 0 3
3 0 0 0 4
4 0 0 0 5
5 0 0 0 6
6 0 0 0 7
7 0 0 0 8
0 1 0 0 9
1 1 0 0 10
2 1 0 0 11
3 1 0 0 12
4 1 0 0 13
5 1 0 0 14
6 1 0 0 15
7 1 0 0 16
0 2 0 0 17
1 2 0 0 18
2 2 0 0 19
3 2 0 0 20
4 2 0 0 21
5 2 0 0 22
6 2 0 0 23
7 2 0 0 24
0 3 0 0 25
1 3 0 0 26
2 3 0 0 27
3 3 0 0 28
4 3 0 0 29
5 3 0 0 30
6 3 0 0 31
7 3 0 0 32
0 4 0 0 33
1 4 0 0 34
2 4 0 0 35
3 4 0 0 36
4 4 0 0 37
5 4 0 0 38
6 4 0 0 39
7 4 0 0 40
0 5 0 0 41
1 5 0 0 42
2 5 0 0 43
3 5 0 0 44
4 5 0 0 45
5 5 0 0 46
6 5 0 0 47
7 5 0 0 48
0 6 0 0 49
1 6 0 0 50
2 6 0 0 51
3 6 0 0 52
4 6 0 0 53
5 6 0 0 54
6 6 0 0 55
7 6 0 0 56
0 7 0 0 57
1 7 0 0 58
2 7 0 0 59
3 7 0 0 60
4 7 0 0 61
5 7 0 0 62
6 7 0 0 63
7 7 0 0 64
0 0 1 0 65
1 0 1 0 66
2 0 1 0 67
3 0 1 0 68
4 0 1 0 69
5 0 1 0 70
6 0 1 0 71
7 0 1 0 72
0 1 1 0 73
1 1 1 0 74
2 1 1 0 75
3 1 1 0 76
4 1 1 0 77
5 1 1 0 78
6 1 1 0 79
7 1 1 0 80
0 2 1 0 81
1 2 1 0 82
2 2 1 0 83
3 2 1 0 84
4 2 1 0 85
5 2 1 0 86
6 2 1 0 87
7 2 1 0 88
0 3 1 0 89
1 3 1 0 90
2 3 1 0 91
3 3 1 0 92
4 3 1 0 93
5 3 1 0 94
6 3 1 0 95
7 3 1 0 96
0 4 1 0 97
1 4 1 0 98
2 4 1 0 99
3 4 1 0 100
4 4 1 0 101
5 4 1 0 102
6 4 1 0 103
7 4 1 0 104
0 5 1 0 105
1 5 1 0 106
2 5 1 0 107
3 5 1 0 108
4 5 1 0 109
5 5 1 0 110
6 5 1 0 111
7 5 1 0 112
0 6 1 0 113
1 6 1 0 114
2 6 1 0 115
3 6 1 0 116
4 6 1 0 117
5 6 1 0 118
6 6 1 0 119
7 6 1 0 120
0 7 1 0 121
1 7 1 0 122
2 7 1 0 123
3 7 1 0 124
4 7 1 0 125
5 7 1 0 126
6 7 1 0 127
7 7 1 0 128
0 0 2 0 129
1 0 2 0 130
2 0 2 0 131
3 0 2 0 132
4 0 2 0 133
5 0 2 0 134
6 0 2 0 135
7 0 2 0 136
0 1 2 0 137
1 1 2 0 138
2 1 2 0 139
3 1 2 0 140
4 1 2 0 141
5 1 2 0 142
6 1 2 0 143
7 1 2 0 144
0 2 2 0 145
1 2 2 0 146
2 2 2 0 147
3 2 2 0 148
4 2 2 0 149
5 2 2 0 150
6 2 2 0 151
7 2 2 0 152
0 3 2 0 153
1 3 2 0 154
2 3 2 0 155
3 3 2 0 156
4 3 2 0 157
5 3 2 0 158
6 3 2 0 159
7 3 2 0 160
0 4 2 0 161
1 4 2 0 162
2 4 2 0 163
3 4 2 0 164
4 4 2 0 165
5 4 2 0 166
6 4 2 0 167
7 4 2 0 168
0 5 2 0 169
1 5 2 0 170
2 5 2 0 171
3 5 2 0 172
4 5 2 0 173
5 5 2 0 174
6 5 2 0 175
7 5 2 0 176
0 6 2 0 177
1 6 2 0 178
2 6 2 0 179
3 6 2 0 180
4 6 2 0 181
5 6 2 0 182
6 6 2 0 183
7 6 2 0 184
0 7 2 0 185
1 7 2 0 186
2 7 2 0 187
3 7 2 0 188
4 7 2 0 189
5 7 2 0 190
6 7 2 0 191
7 7 2 0 192
0 0 3 0 193
1 0 3 0 194
2 0 3 0 195
3 0 3 0 196
4 0 3 0 197
5 0 3 0 198
6 0 3 0 199
7 0 3 0 200
0 1 3 0 201
1 1 3 0 202
2 1 3 0 203
3 1 3 0 204
4 1 3 0 205
5 1 3 0 206
6 1 3 0 207
7 1 3 0 208
0 2 3 0 209
1 2 3 0 210
2 2 3 0 211
3 2 3 0 212
4 2 3 0 213
5 2 3 0 214
6 2 3 0 215
7 2 3 0 216
0 3 3 0 217
1 3 3 0 218
2 3 3 0 219
3 3 3 0 220
4 3 3 0 221
5 3 3 0 222
6 3 3 0 223
7 3 3 0 224
0 4 3 0 225
1 4 3 0 226
2 4 3 0 227
3 4 3 0 228
4 4 3 0 229
5 4 3 0 230
6 4 3 0 231
7 4 3 0 232
0 5 3 0 233
1 5 3 0 234
2 5 3 0 235
3 5 3 0 236
4 5 3 0 237
5 5 3 0 238
6 5 3 0 239
7 5 3 0 240
0 6 3 0 241
1 6 3 0 242
2 6 3 0 243
3 6 3 0 244
4 6 3 0 245
5 6 3 0 246
6 6 3 0 247
7 6 3 0 248
0 7 3 0 249
1 7 3 0 250
2 7 3 0 251
3 7 3 0 252
4 7 3 0 253
5 7 3 0 254
6 7 3 0 255
7 7 3 0 256
0 0 4 0 257
1 0 4 0 258
2 0 4 0 259
3 0 4 0 260
4 0 4 0 261
5 0 4 0 262
6 0 4 0 263
7 0 4 0 264
0 1 4 0 265
1 1 4 0 266
2 1 4 0 267
3 1 4 0 268
4 1 4 0 269
5 1 4 0 270
6 1 4 0 271
7 1 4 0 272
0 2 4 0 273
1 2 4 0 274
2 2 4 0 275
3 2 4 0 276
4 2 4 0 277
5 2 4 0 278
6 2 4 0 279
7 2 4 0 280
0 3 4 0 281
1 3 4 0 282
2 3 4 0 283
3 3 4 0 284
4 3 4 0 285
5 3 4 0 286
6 3 4 0 287
7 3 4 0 288
0 4 4 0 289
1 4 4 0 290
2 4 4 0 291
3 4 4 0 292
4 4 4 0 293
5 4 4 0 294
6 4 4 0 295
7 4 4 0 296
0 5 4 0 297
1 5 4 0 298
2 5 4 0 299
3 5 4 0 300
4 5 4 0 301
5 5 4 0 302
6 5 4 0 303
7 5 4 0 304
0 6 4 0 305
1 6 4 0 306
2 6 4 0 307
3 6 4 0 308
4 6 4 0 309
5 6 4 0 310
6 6 4 0 311
7 6 4 0 312
0 7 4 0 313
1 7 4 0 314
2 7 4 0 315
3 7 4 0 316
4 7 4 0 317
5 7 4 0 318
6 7 4 0 319
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end
showpage
%%Trailer
%%DocumentFonts: Symbol Helvetica
%%Pages: 1

18
examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp Normal file
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@ -0,0 +1,18 @@
set term post enha colo 20
set out 'pdisp.eps'
set xlabel 'q'
set ylabel '{/Symbol n} (THz)'
set xtics ("{/Symbol G}" 0., "X" 0.7071, "W" 1.06066, "X'" 1.41421, "{/Symbol G}" 2.63896, "L" 3.50498)
set xr [0:3.50498]
set yr [0:8.5]
set key at 3.0,8.2
set grid xtics lt 9
plot './disp-ld.dat' u 2:6 w l lt -1 t 'LD',\
'' u 2:7 w l lt -1 t '', \
'' u 2:8 w l lt -1 t '',\
'./disp.dat' u 4:5 w p pt 7 lt 1 t 'MD',\
'' u 4:6 w p pt 7 lt 1 t '',\
'' u 4:7 w p pt 7 lt 1 t '', \
'disp-expr.dat' u 5:2 w p pt 5 lt 3 t 'expr'

13
examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos Normal file
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@ -0,0 +1,13 @@
set term post enha colo 20
set out 'pdos.eps'
set xlabel '{/Symbol n} (THz)'
set ylabel 'g({/Symbol n})'
set xr [0:8]
set yr [0:0.5]
set key top left
unset ytics
plot 'dos-ld.dat' u 1:2 w l lt -1 t 'LD',\
'dos.dat' u 1:2 w l lt 2 lw 2 t 'MD',\
'dos-expr.dat' u 1:2 w l lt 3 lw 2 t 'expr'