forked from lijiext/lammps
Now using mix and match syntax
This commit is contained in:
Aidan Thompson
parent
b5dfdc4fa4
commit
47709c4cad
|
|
@ -1,4 +1,4 @@
|
|||
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
# DATE: 2020-04-04 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
|
@ -11,7 +11,7 @@ variable zblz equal 73
|
|||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
snap
|
||||
mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
|
||||
pair_coeff * * mliap Ta
|
||||
|
||||
|
|
@ -6,9 +6,16 @@
|
|||
rcutfac 4.67637
|
||||
twojmax 6
|
||||
|
||||
# elements
|
||||
|
||||
nelems 1
|
||||
elems Ta
|
||||
radelems 0.5
|
||||
welems 1
|
||||
|
||||
# optional
|
||||
|
||||
rfac0 0.99363
|
||||
rmin0 0
|
||||
bzeroflag 0
|
||||
quadraticflag 0
|
||||
|
||||
|
|
@ -2,8 +2,8 @@
|
|||
|
||||
# LAMMPS SNAP coefficients for Ta_Cand06A
|
||||
|
||||
# nelements ncoeff
|
||||
1 31
|
||||
Ta 0.5 1
|
||||
-2.92477
|
||||
-0.01137
|
||||
-0.00775
|
||||
|
|
@ -1,5 +1,3 @@
|
|||
#
|
||||
#
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
|
|
@ -9,7 +7,7 @@ variable zblz equal 74
|
|||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
snap
|
||||
mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * snap W.quadratic.snapcoeff W.quadratic.snapparam W
|
||||
pair_coeff * * mliap W
|
||||
|
||||
|
|
@ -1,10 +1,18 @@
|
|||
# required
|
||||
|
||||
rcutfac 4.73442
|
||||
twojmax 6
|
||||
|
||||
# elements
|
||||
|
||||
nelems 1
|
||||
elems W
|
||||
radelems 0.5
|
||||
welems 1
|
||||
|
||||
# optional
|
||||
|
||||
rfac0 0.99363
|
||||
rmin0 0
|
||||
bzeroflag 1
|
||||
quadraticflag 1
|
||||
|
||||
|
|
@ -1,7 +1,7 @@
|
|||
# LAMMPS SNAP coefficients for Quadratic W
|
||||
|
||||
# nelements ncoeff
|
||||
1 496
|
||||
W 0.5 1
|
||||
0.000000000000
|
||||
-0.000019342340
|
||||
0.000039964908
|
||||
|
|
@ -0,0 +1,16 @@
|
|||
# DATE: 2020-04-04 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz1 equal 74
|
||||
variable zblz2 equal 4
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} &
|
||||
mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff * * mliap W Be
|
||||
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
# required
|
||||
|
||||
rcutfac 4.8123
|
||||
twojmax 8
|
||||
|
||||
# elements
|
||||
|
||||
nelems 2
|
||||
elems W Be
|
||||
radelems 0.5 0.417932
|
||||
welems 1 0.959049
|
||||
|
||||
# optional
|
||||
|
||||
rfac0 0.99363
|
||||
rmin0 0
|
||||
bzeroflag 1
|
||||
|
||||
|
|
@ -0,0 +1,116 @@
|
|||
# LAMMPS SNAP coefficients for WBe
|
||||
|
||||
# nelements ncoeff
|
||||
2 56
|
||||
-0.000000000000 # B[0]
|
||||
-0.001487061994 # B[1, 0, 0, 0]
|
||||
0.075808306870 # B[2, 1, 0, 1]
|
||||
0.538735683870 # B[3, 1, 1, 2]
|
||||
-0.074148039366 # B[4, 2, 0, 2]
|
||||
0.602629813770 # B[5, 2, 1, 3]
|
||||
-0.147022424344 # B[6, 2, 2, 2]
|
||||
0.117756828488 # B[7, 2, 2, 4]
|
||||
-0.026490439049 # B[8, 3, 0, 3]
|
||||
-0.035162708767 # B[9, 3, 1, 4]
|
||||
0.064315385091 # B[10, 3, 2, 3]
|
||||
-0.131936948089 # B[11, 3, 2, 5]
|
||||
-0.021272860272 # B[12, 3, 3, 4]
|
||||
-0.091171134054 # B[13, 3, 3, 6]
|
||||
-0.024396224398 # B[14, 4, 0, 4]
|
||||
-0.059813132803 # B[15, 4, 1, 5]
|
||||
0.069585393203 # B[16, 4, 2, 4]
|
||||
-0.085344044181 # B[17, 4, 2, 6]
|
||||
-0.155425254597 # B[18, 4, 3, 5]
|
||||
-0.117031758367 # B[19, 4, 3, 7]
|
||||
-0.040956258020 # B[20, 4, 4, 4]
|
||||
-0.084465000389 # B[21, 4, 4, 6]
|
||||
-0.020367513630 # B[22, 4, 4, 8]
|
||||
-0.010730484318 # B[23, 5, 0, 5]
|
||||
-0.054777575658 # B[24, 5, 1, 6]
|
||||
0.050742893747 # B[25, 5, 2, 5]
|
||||
-0.004686334611 # B[26, 5, 2, 7]
|
||||
-0.116372907121 # B[27, 5, 3, 6]
|
||||
0.005542497708 # B[28, 5, 3, 8]
|
||||
-0.126526795635 # B[29, 5, 4, 5]
|
||||
-0.080163926221 # B[30, 5, 4, 7]
|
||||
-0.082426250179 # B[31, 5, 5, 6]
|
||||
-0.010558777281 # B[32, 5, 5, 8]
|
||||
-0.001939058038 # B[33, 6, 0, 6]
|
||||
-0.027907949962 # B[34, 6, 1, 7]
|
||||
0.049483908476 # B[35, 6, 2, 6]
|
||||
0.005103754385 # B[36, 6, 2, 8]
|
||||
-0.054751505141 # B[37, 6, 3, 7]
|
||||
-0.055556071011 # B[38, 6, 4, 6]
|
||||
-0.006026917619 # B[39, 6, 4, 8]
|
||||
-0.060889030109 # B[40, 6, 5, 7]
|
||||
-0.029977673973 # B[41, 6, 6, 6]
|
||||
-0.014987527280 # B[42, 6, 6, 8]
|
||||
-0.006697686658 # B[43, 7, 0, 7]
|
||||
0.017369624409 # B[44, 7, 1, 8]
|
||||
0.047864358817 # B[45, 7, 2, 7]
|
||||
-0.001989812679 # B[46, 7, 3, 8]
|
||||
0.000153530925 # B[47, 7, 4, 7]
|
||||
-0.003862356345 # B[48, 7, 5, 8]
|
||||
-0.009754314198 # B[49, 7, 6, 7]
|
||||
0.000777958970 # B[50, 7, 7, 8]
|
||||
-0.003031424287 # B[51, 8, 0, 8]
|
||||
0.015612715209 # B[52, 8, 2, 8]
|
||||
0.003210129646 # B[53, 8, 4, 8]
|
||||
-0.013088799947 # B[54, 8, 6, 8]
|
||||
0.001465970755 # B[55, 8, 8, 8]
|
||||
0.000000000000 # B[0]
|
||||
-0.000112143918 # B[1, 0, 0, 0]
|
||||
0.002449805180 # B[2, 1, 0, 1]
|
||||
0.189705916830 # B[3, 1, 1, 2]
|
||||
-0.019967429692 # B[4, 2, 0, 2]
|
||||
0.286015704682 # B[5, 2, 1, 3]
|
||||
0.072864063124 # B[6, 2, 2, 2]
|
||||
0.108748154196 # B[7, 2, 2, 4]
|
||||
-0.005203284351 # B[8, 3, 0, 3]
|
||||
0.043948598532 # B[9, 3, 1, 4]
|
||||
0.105425889093 # B[10, 3, 2, 3]
|
||||
0.060460134045 # B[11, 3, 2, 5]
|
||||
-0.003406205141 # B[12, 3, 3, 4]
|
||||
0.002306765306 # B[13, 3, 3, 6]
|
||||
-0.003845115174 # B[14, 4, 0, 4]
|
||||
0.029471162073 # B[15, 4, 1, 5]
|
||||
0.054901130330 # B[16, 4, 2, 4]
|
||||
0.010910192753 # B[17, 4, 2, 6]
|
||||
0.033885210622 # B[18, 4, 3, 5]
|
||||
0.008053439551 # B[19, 4, 3, 7]
|
||||
-0.001432298168 # B[20, 4, 4, 4]
|
||||
0.017478027729 # B[21, 4, 4, 6]
|
||||
-0.003402034990 # B[22, 4, 4, 8]
|
||||
-0.002655339820 # B[23, 5, 0, 5]
|
||||
0.012668749892 # B[24, 5, 1, 6]
|
||||
0.037521561888 # B[25, 5, 2, 5]
|
||||
-0.000682693314 # B[26, 5, 2, 7]
|
||||
0.008525913627 # B[27, 5, 3, 6]
|
||||
0.008977936348 # B[28, 5, 3, 8]
|
||||
0.006922732235 # B[29, 5, 4, 5]
|
||||
0.003031883044 # B[30, 5, 4, 7]
|
||||
-0.000345577975 # B[31, 5, 5, 6]
|
||||
-0.001041600679 # B[32, 5, 5, 8]
|
||||
-0.001407625493 # B[33, 6, 0, 6]
|
||||
0.004211558640 # B[34, 6, 1, 7]
|
||||
0.014450875461 # B[35, 6, 2, 6]
|
||||
-0.007033326252 # B[36, 6, 2, 8]
|
||||
0.004998742185 # B[37, 6, 3, 7]
|
||||
-0.002824617682 # B[38, 6, 4, 6]
|
||||
0.003831871934 # B[39, 6, 4, 8]
|
||||
-0.005700892700 # B[40, 6, 5, 7]
|
||||
0.000184422409 # B[41, 6, 6, 6]
|
||||
0.001592696824 # B[42, 6, 6, 8]
|
||||
-0.000804927645 # B[43, 7, 0, 7]
|
||||
0.008465358642 # B[44, 7, 1, 8]
|
||||
0.005460531160 # B[45, 7, 2, 7]
|
||||
-0.000639605094 # B[46, 7, 3, 8]
|
||||
-0.002403948393 # B[47, 7, 4, 7]
|
||||
-0.001267042453 # B[48, 7, 5, 8]
|
||||
0.003836940623 # B[49, 7, 6, 7]
|
||||
0.002333141437 # B[50, 7, 7, 8]
|
||||
-0.000665360637 # B[51, 8, 0, 8]
|
||||
-0.003460637865 # B[52, 8, 2, 8]
|
||||
-0.001598726043 # B[53, 8, 4, 8]
|
||||
0.001478744304 # B[54, 8, 6, 8]
|
||||
0.000806643203 # B[55, 8, 8, 8]
|
||||
|
|
@ -1,11 +0,0 @@
|
|||
ITEM: TIMESTEP
|
||||
0
|
||||
ITEM: NUMBER OF ATOMS
|
||||
2
|
||||
ITEM: BOX BOUNDS pp pp pp
|
||||
0.0000000000000000e+00 3.1802999999999999e+00
|
||||
0.0000000000000000e+00 3.1802999999999999e+00
|
||||
0.0000000000000000e+00 3.1802999999999999e+00
|
||||
ITEM: ATOMS id type fx fy fz c_eatom
|
||||
1 1 -0.00995108 -0.61461 0.688381 -1.15754
|
||||
2 1 0.00995108 0.61461 -0.688381 -1.15754
|
||||
|
|
@ -1,11 +0,0 @@
|
|||
ITEM: TIMESTEP
|
||||
100
|
||||
ITEM: NUMBER OF ATOMS
|
||||
2
|
||||
ITEM: BOX BOUNDS pp pp pp
|
||||
0.0000000000000000e+00 3.1802999999999999e+00
|
||||
0.0000000000000000e+00 3.1802999999999999e+00
|
||||
0.0000000000000000e+00 3.1802999999999999e+00
|
||||
ITEM: ATOMS id type fx fy fz c_eatom
|
||||
1 1 -0.373431 0.0494017 -1.17879 -1.14648
|
||||
2 1 0.373431 -0.0494017 1.17879 -1.14648
|
||||
|
|
@ -24,10 +24,18 @@ mass 1 180.88
|
|||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.snap
|
||||
include Ta06A.mliap
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
|
|
@ -1,10 +1,10 @@
|
|||
# Demonstrate SNAP Ta potential
|
||||
# Demonstrate SNAP W-Be potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
|
@ -17,29 +17,28 @@ boundary p p p
|
|||
|
||||
lattice bcc $a
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
create_box 1 box
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass 1 183.84
|
||||
mass 2 9.012182
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
group tungsten type 1
|
||||
group beryllium type 2
|
||||
# choose potential
|
||||
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
mliap/snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * mliap/snap Ta06A.snapcoeff Ta06A.snapparam Ta
|
||||
include WBe_Wood_PRB2019.mliap
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
|
|
@ -25,15 +25,20 @@ mass 1 183.84
|
|||
|
||||
# choose potential
|
||||
|
||||
include W.snap.quadratic
|
||||
include W.quadratic.mliap
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
compute eatom all pe/atom
|
||||
|
||||
dump 1 all custom 100 dump.quadratic.* id type fx fy fz c_eatom
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
|
|
@ -1,60 +0,0 @@
|
|||
# Demonstrate SNAP Ta potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 1
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable ny equal ${nrep}
|
||||
variable nz equal ${nrep}
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
displace_atoms all random 0.01 0.01 0.01 12345
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
# choose potential
|
||||
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 74
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
mliap/snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * mliap/snap W.quadratic.snapcoeff W.quadratic.snapparam W
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
compute eatom all pe/atom
|
||||
|
||||
dump 1 all custom 100 dump.quadratic.* id type fx fy fz c_eatom
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check no
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
|
@ -1,100 +0,0 @@
|
|||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
||||
variable nsteps index 0
|
||||
variable nrep equal 1
|
||||
variable a equal 2.0
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable ny equal ${nrep}
|
||||
variable nz equal ${nrep}
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
create_box 2 box
|
||||
create_atoms 2 box
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 1
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string &
|
||||
"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
|
||||
# set up dummy potential to satisfy cutoff
|
||||
|
||||
pair_style zero ${rcutfac}
|
||||
pair_coeff * *
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute db all snad/atom ${snap_options}
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
group snapgroup2 type 2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_120 equal c_db[2][120]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
compute snap all snap ${snap_options}
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
|
||||
# 4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom &
|
||||
pe pxy c_bsum2[20] c_vbsum[240] v_db_2_120 &
|
||||
c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
# dump_modify mydump_db sort id
|
||||
|
||||
# Run MD
|
||||
|
||||
run ${nsteps}
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
LAMMPS (19 Mar 2020)
|
||||
# Demonstrate SNAP Ta potential
|
||||
|
||||
# Initialize simulation
|
||||
|
|
@ -7,7 +6,7 @@ LAMMPS (27 Nov 2018)
|
|||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
|
|
@ -18,21 +17,21 @@ variable ny equal 4
|
|||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000350714 secs
|
||||
create_atoms CPU = 0.000254 secs
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
|
|
@ -56,7 +55,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
|
|||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 73 ${zblz}
|
||||
pair_coeff 1 1 zbl 73 73
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
|
||||
Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
|
||||
SNAP Element = Ta, Radius 0.5, Weight 1
|
||||
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
|
||||
|
|
@ -64,14 +63,21 @@ SNAP keyword rcutfac 4.67637
|
|||
SNAP keyword twojmax 6
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword diagonalstyle 3
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
|
@ -103,33 +109,33 @@ Neighbor list info ...
|
|||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.85157 0 -11.813095 2717.1661
|
||||
10 295.96579 -11.851053 0 -11.813095 2696.1559
|
||||
20 284.32535 -11.84956 0 -11.813095 2301.3713
|
||||
30 266.04602 -11.847215 0 -11.813095 1832.1745
|
||||
40 242.2862 -11.844168 0 -11.813095 1492.6765
|
||||
50 214.48968 -11.840603 0 -11.813094 1312.8908
|
||||
60 184.32523 -11.836734 0 -11.813094 1284.582
|
||||
70 153.58055 -11.832791 0 -11.813094 1374.4457
|
||||
80 124.04276 -11.829003 0 -11.813094 1537.703
|
||||
90 97.37622 -11.825582 0 -11.813094 1734.9662
|
||||
100 75.007873 -11.822714 0 -11.813094 1930.8005
|
||||
Loop time of 5.03244 on 1 procs for 100 steps with 128 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.591 | 6.591 | 6.591 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
||||
10 295.96579 -11.851053 -11.851053 -11.813095 2696.1559 -2696.1559
|
||||
20 284.32535 -11.84956 -11.84956 -11.813095 2301.3713 -2301.3713
|
||||
30 266.04602 -11.847215 -11.847215 -11.813095 1832.1745 -1832.1745
|
||||
40 242.2862 -11.844168 -11.844168 -11.813095 1492.6765 -1492.6765
|
||||
50 214.48968 -11.840603 -11.840603 -11.813094 1312.8908 -1312.8908
|
||||
60 184.32523 -11.836734 -11.836734 -11.813094 1284.582 -1284.582
|
||||
70 153.58055 -11.832791 -11.832791 -11.813094 1374.4457 -1374.4457
|
||||
80 124.04276 -11.829003 -11.829003 -11.813094 1537.703 -1537.703
|
||||
90 97.37622 -11.825582 -11.825582 -11.813094 1734.9662 -1734.9662
|
||||
100 75.007873 -11.822714 -11.822714 -11.813094 1930.8005 -1930.8005
|
||||
Loop time of 0.995328 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.858 ns/day, 27.958 hours/ns, 19.871 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 4.340 ns/day, 5.530 hours/ns, 100.469 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.0308 | 5.0308 | 5.0308 | 0.0 | 99.97
|
||||
Pair | 0.99426 | 0.99426 | 0.99426 | 0.0 | 99.89
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00070858 | 0.00070858 | 0.00070858 | 0.0 | 0.01
|
||||
Output | 0.00024676 | 0.00024676 | 0.00024676 | 0.0 | 0.00
|
||||
Modify | 0.0002749 | 0.0002749 | 0.0002749 | 0.0 | 0.01
|
||||
Other | | 0.0004299 | | | 0.01
|
||||
Comm | 0.000305 | 0.000305 | 0.000305 | 0.0 | 0.03
|
||||
Output | 0.000413 | 0.000413 | 0.000413 | 0.0 | 0.04
|
||||
Modify | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.02
|
||||
Other | | 0.000191 | | | 0.02
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -145,4 +151,4 @@ Ave neighs/atom = 58
|
|||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:05
|
||||
Total wall time: 0:00:01
|
||||
|
|
|
|||
|
|
@ -0,0 +1,163 @@
|
|||
LAMMPS (19 Mar 2020)
|
||||
# Demonstrate SNAP W-Be potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000231 secs
|
||||
mass 1 183.84
|
||||
mass 2 9.012182
|
||||
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fraction
|
||||
group tungsten type 1
|
||||
123 atoms in group tungsten
|
||||
group beryllium type 2
|
||||
5 atoms in group beryllium
|
||||
# choose potential
|
||||
|
||||
include WBe_Wood_PRB2019.snap
|
||||
# DATE: 2019-09-18 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz1 equal 74
|
||||
variable zblz2 equal 4
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 4.8 snap
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 1 zbl 74 ${zblz1}
|
||||
pair_coeff 1 1 zbl 74 74
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 1 2 zbl 74 ${zblz2}
|
||||
pair_coeff 1 2 zbl 74 4
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff 2 2 zbl 4 ${zblz2}
|
||||
pair_coeff 2 2 zbl 4 4
|
||||
pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
|
||||
SNAP Element = W, Radius 0.5, Weight 1
|
||||
SNAP Element = Be, Radius 0.417932, Weight 0.959049
|
||||
SNAP keyword rcutfac 4.8123
|
||||
SNAP keyword twojmax 8
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 1
|
||||
SNAP keyword quadraticflag 0
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.8123
|
||||
ghost atom cutoff = 5.8123
|
||||
binsize = 2.90615, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair snap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.893 | 6.893 | 6.893 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -8.5980876 -8.5980876 -8.5596125 -35284.855 35284.855
|
||||
10 299.29029 -8.5979965 -8.5979965 -8.5596125 -35299.259 35299.259
|
||||
20 288.99334 -8.5966759 -8.5966759 -8.5596124 -35004.093 35004.093
|
||||
30 269.91027 -8.5942284 -8.5942284 -8.5596123 -34447.077 34447.077
|
||||
40 243.57361 -8.5908505 -8.5908505 -8.5596121 -33687.105 33687.105
|
||||
50 212.21385 -8.5868284 -8.5868284 -8.5596119 -32821.864 32821.864
|
||||
60 178.77144 -8.5825391 -8.5825391 -8.5596116 -31971.17 31971.17
|
||||
70 146.71854 -8.578428 -8.578428 -8.5596113 -31245.51 31245.51
|
||||
80 119.50956 -8.5749383 -8.5749383 -8.5596111 -30724.137 30724.137
|
||||
90 99.872785 -8.5724197 -8.5724197 -8.559611 -30440.244 30440.244
|
||||
100 89.604584 -8.5711027 -8.5711027 -8.5596109 -30392.805 30392.805
|
||||
Loop time of 3.17984 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 1.359 ns/day, 17.666 hours/ns, 31.448 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.1748 | 3.1748 | 3.1748 | 0.0 | 99.84
|
||||
Neigh | 0.000314 | 0.000314 | 0.000314 | 0.0 | 0.01
|
||||
Comm | 0.000371 | 0.000371 | 0.000371 | 0.0 | 0.01
|
||||
Output | 0.00386 | 0.00386 | 0.00386 | 0.0 | 0.12
|
||||
Modify | 0.000236 | 0.000236 | 0.000236 | 0.0 | 0.01
|
||||
Other | | 0.000289 | | | 0.01
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3710 ave 3710 max 3710 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7420 ave 7420 max 7420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7420
|
||||
Ave neighs/atom = 57.9688
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -31,7 +31,7 @@ Created orthogonal box = (0 0 0) to (3.1803 3.1803 3.1803)
|
|||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.000348 secs
|
||||
create_atoms CPU = 0.000215 secs
|
||||
displace_atoms all random 0.01 0.01 0.01 12345
|
||||
|
||||
mass 1 183.84
|
||||
|
|
@ -66,9 +66,16 @@ SNAP keyword quadraticflag 1
|
|||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
compute eatom all pe/atom
|
||||
|
||||
dump 1 all custom 100 dump.quadratic.* id type fx fy fz c_eatom
|
||||
|
||||
|
|
@ -101,33 +108,33 @@ Neighbor list info ...
|
|||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.04 | 5.04 | 5.04 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -1.1575362 0 -1.1381472 600966
|
||||
10 349.32287 -1.1607243 0 -1.1381475 599985.48
|
||||
20 384.27065 -1.1629832 0 -1.1381478 599287.89
|
||||
30 399.34846 -1.1639578 0 -1.1381478 598986.42
|
||||
40 392.19413 -1.1634953 0 -1.1381478 599130.05
|
||||
50 363.93932 -1.161669 0 -1.1381476 599694.93
|
||||
60 319.03014 -1.1587663 0 -1.1381473 600588.89
|
||||
70 264.53512 -1.1552439 0 -1.138147 601667.76
|
||||
80 209.04294 -1.1516571 0 -1.1381466 602760.01
|
||||
90 161.3157 -1.1485722 0 -1.1381463 603694.49
|
||||
100 128.9054 -1.1464773 0 -1.1381461 604326.7
|
||||
Loop time of 0.032082 on 1 procs for 100 steps with 2 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.284 | 7.284 | 7.284 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -1.1575362 -1.1575362 -1.1381472 600966 -600966
|
||||
10 349.32287 -1.1607243 -1.1607243 -1.1381475 599985.48 -599985.48
|
||||
20 384.27065 -1.1629832 -1.1629832 -1.1381478 599287.89 -599287.89
|
||||
30 399.34846 -1.1639578 -1.1639578 -1.1381478 598986.42 -598986.42
|
||||
40 392.19413 -1.1634953 -1.1634953 -1.1381478 599130.05 -599130.05
|
||||
50 363.93932 -1.161669 -1.161669 -1.1381476 599694.93 -599694.93
|
||||
60 319.03014 -1.1587663 -1.1587663 -1.1381473 600588.89 -600588.89
|
||||
70 264.53512 -1.1552439 -1.1552439 -1.138147 601667.76 -601667.76
|
||||
80 209.04294 -1.1516571 -1.1516571 -1.1381466 602760.01 -602760.01
|
||||
90 161.3157 -1.1485722 -1.1485722 -1.1381463 603694.49 -603694.49
|
||||
100 128.9054 -1.1464773 -1.1464773 -1.1381461 604326.7 -604326.7
|
||||
Loop time of 0.030198 on 1 procs for 100 steps with 2 atoms
|
||||
|
||||
Performance: 134.655 ns/day, 0.178 hours/ns, 3117.013 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 143.056 ns/day, 0.168 hours/ns, 3311.478 timesteps/s
|
||||
98.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.030667 | 0.030667 | 0.030667 | 0.0 | 95.59
|
||||
Neigh | 0.000584 | 0.000584 | 0.000584 | 0.0 | 1.82
|
||||
Comm | 0.000307 | 0.000307 | 0.000307 | 0.0 | 0.96
|
||||
Output | 0.000447 | 0.000447 | 0.000447 | 0.0 | 1.39
|
||||
Modify | 2.8e-05 | 2.8e-05 | 2.8e-05 | 0.0 | 0.09
|
||||
Other | | 4.9e-05 | | | 0.15
|
||||
Pair | 0.028723 | 0.028723 | 0.028723 | 0.0 | 95.12
|
||||
Neigh | 0.000515 | 0.000515 | 0.000515 | 0.0 | 1.71
|
||||
Comm | 0.000263 | 0.000263 | 0.000263 | 0.0 | 0.87
|
||||
Output | 0.000618 | 0.000618 | 0.000618 | 0.0 | 2.05
|
||||
Modify | 2.7e-05 | 2.7e-05 | 2.7e-05 | 0.0 | 0.09
|
||||
Other | | 5.2e-05 | | | 0.17
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
|
|||
Loading…
Reference in New Issue