Fixed error in compute snap for quadratic and add log files for regression testing
This commit is contained in:
Aidan Thompson
@ -4,7 +4,6 @@
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variable nsteps index 0
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variable nsteps index 0
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variable nrep equal 1
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variable nrep equal 1
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#variable a equal 3.316
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variable a equal 2.0
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variable a equal 2.0
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units metal
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units metal
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@ -16,6 +15,7 @@ variable nz equal ${nrep}
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boundary p p p
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boundary p p p
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atom_modify map hash
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lattice bcc $a
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lattice bcc $a
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 2 box
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create_box 2 box
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@ -35,8 +35,11 @@ variable radelem1 equal 2.3
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variable radelem2 equal 2.0
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variable radelem2 equal 2.0
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variable wj1 equal 1.0
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variable wj1 equal 1.0
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variable wj2 equal 0.96
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variable wj2 equal 0.96
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variable quadratic equal 0
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variable bzero equal 0
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variable switch equal 0
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variable snap_options string &
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variable snap_options string &
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"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0"
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"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
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# set up dummy potential to satisfy cutoff
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# set up dummy potential to satisfy cutoff
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@ -67,6 +70,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
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# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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compute vbsum all reduce sum c_vb[*]
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compute vbsum all reduce sum c_vb[*]
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# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
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# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
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variable db_2_30 equal c_db[2][30]
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# set up compute snap generating global array
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# set up compute snap generating global array
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@ -78,12 +82,14 @@ thermo 100
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# test output: 1: total potential energy
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# test output: 1: total potential energy
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# 2: xy component of stress tensor
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# 2: xy component of stress tensor
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# 3: Sum(B_{000}^i, all i of type 2)
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# 3: Sum(B_{000}^i, all i of type 2)
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# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dr_j), all i of type 2), all j)
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# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
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# followed by counterparts from compute snap
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# 5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
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#
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# followed by 5 counterparts from compute snap
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thermo_style custom &
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thermo_style custom &
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pe pxy c_bsum2[1] c_vbsum[60] &
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pe pxy c_bsum2[1] c_vbsum[60] v_db_2_30 &
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c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10]
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c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
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thermo_modify norm no
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thermo_modify norm no
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# dump mydump_db all custom 1000 dump_db id c_db[*]
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# dump mydump_db all custom 1000 dump_db id c_db[*]
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100
examples/snap/in.snap.compute.quadratic
Normal file
100
examples/snap/in.snap.compute.quadratic
Normal file
@ -0,0 +1,100 @@
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# Demonstrate bispectrum computes
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# initialize simulation
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variable nsteps index 0
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variable nrep equal 1
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variable a equal 2.0
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable ny equal ${nrep}
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variable nz equal ${nrep}
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boundary p p p
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atom_modify map hash
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lattice bcc $a
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 2 box
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create_atoms 2 box
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mass * 180.88
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displace_atoms all random 0.1 0.1 0.1 123456
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# choose SNA parameters
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variable twojmax equal 2
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variable rcutfac equal 1.0
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable radelem1 equal 2.3
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variable radelem2 equal 2.0
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variable wj1 equal 1.0
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variable wj2 equal 0.96
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variable quadratic equal 1
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variable bzero equal 0
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variable switch equal 0
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variable snap_options string &
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"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
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# set up dummy potential to satisfy cutoff
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pair_style zero ${rcutfac}
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pair_coeff * *
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# set up reference potential
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style zbl ${zblcutinner} ${zblcutouter}
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pair_coeff * * ${zblz} ${zblz}
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# set up per-atom computes
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compute b all sna/atom ${snap_options}
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compute vb all snav/atom ${snap_options}
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compute db all snad/atom ${snap_options}
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# perform sums over atoms
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group snapgroup1 type 1
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group snapgroup2 type 2
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compute bsum1 snapgroup1 reduce sum c_b[*]
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compute bsum2 snapgroup2 reduce sum c_b[*]
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# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
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# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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compute vbsum all reduce sum c_vb[*]
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# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
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variable db_2_120 equal c_db[2][120]
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# set up compute snap generating global array
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compute snap all snap ${snap_options}
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fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
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thermo 100
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# test output: 1: total potential energy
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# 2: xy component of stress tensor
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# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
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# 4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
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# 5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
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#
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# followed by 5 counterparts from compute snap
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thermo_style custom &
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pe pxy c_bsum2[20] c_vbsum[240] v_db_2_120 &
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c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
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thermo_modify norm no
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# dump mydump_db all custom 1000 dump_db id c_db[*]
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# dump_modify mydump_db sort id
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# Run MD
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run ${nsteps}
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198
examples/snap/log.27Nov18.snap.compute.g++.1
Normal file
198
examples/snap/log.27Nov18.snap.compute.g++.1
Normal file
@ -0,0 +1,198 @@
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LAMMPS (20 Nov 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate bispectrum computes
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# initialize simulation
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variable nsteps index 0
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variable nrep equal 1
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variable a equal 2.0
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 1
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variable ny equal ${nrep}
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variable ny equal 1
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variable nz equal ${nrep}
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variable nz equal 1
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boundary p p p
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atom_modify map hash
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lattice bcc $a
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lattice bcc 2
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Lattice spacing in x,y,z = 2 2 2
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 1 0 ${ny} 0 ${nz}
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region box block 0 1 0 1 0 ${nz}
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region box block 0 1 0 1 0 1
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create_box 2 box
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Created orthogonal box = (0 0 0) to (2 2 2)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 2 atoms
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create_atoms CPU = 0.000478029 secs
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mass * 180.88
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displace_atoms all random 0.1 0.1 0.1 123456
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# choose SNA parameters
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variable twojmax equal 2
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variable rcutfac equal 1.0
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable radelem1 equal 2.3
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variable radelem2 equal 2.0
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variable wj1 equal 1.0
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variable wj2 equal 0.96
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variable quadratic equal 0
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variable bzero equal 0
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variable switch equal 0
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variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
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1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
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# set up dummy potential to satisfy cutoff
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pair_style zero ${rcutfac}
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pair_style zero 1
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pair_coeff * *
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# set up reference potential
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style zbl ${zblcutinner} ${zblcutouter}
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pair_style zbl 4 ${zblcutouter}
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pair_style zbl 4 4.8
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pair_coeff * * ${zblz} ${zblz}
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pair_coeff * * 73 ${zblz}
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pair_coeff * * 73 73
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# set up per-atom computes
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compute b all sna/atom ${snap_options}
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compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
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compute vb all snav/atom ${snap_options}
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compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
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compute db all snad/atom ${snap_options}
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compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
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# perform sums over atoms
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group snapgroup1 type 1
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0 atoms in group snapgroup1
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group snapgroup2 type 2
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2 atoms in group snapgroup2
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compute bsum1 snapgroup1 reduce sum c_b[*]
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compute bsum2 snapgroup2 reduce sum c_b[*]
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# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
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# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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compute vbsum all reduce sum c_vb[*]
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# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
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variable db_2_30 equal c_db[2][30]
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# set up compute snap generating global array
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compute snap all snap ${snap_options}
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compute snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
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fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
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thermo 100
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# test output: 1: total potential energy
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# 2: xy component of stress tensor
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# 3: Sum(B_{000}^i, all i of type 2)
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# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
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# 5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
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#
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# followed by 5 counterparts from compute snap
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thermo_style custom pe pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
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thermo_modify norm no
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# dump mydump_db all custom 1000 dump_db id c_db[*]
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# dump_modify mydump_db sort id
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# Run MD
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run ${nsteps}
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run 0
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.8
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ghost atom cutoff = 6.8
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binsize = 3.4, bins = 1 1 1
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5 neighbor lists, perpetual/occasional/extra = 1 4 0
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(1) pair zbl, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) compute sna/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(3) compute snav/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(4) compute snad/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(5) compute snap, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.06 | 10.06 Mbytes
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PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
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322.86952 1505558.1 364182.88 381.32218 -855.04473 322.86952 1505558.1 364182.88 381.32218 -855.04473
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Loop time of 9.53674e-07 on 1 procs for 0 steps with 2 atoms
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104.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 9.537e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 853 ave 853 max 853 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 330 ave 330 max 330 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 660 ave 660 max 660 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 660
|
||||||
|
Ave neighs/atom = 330
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
199
examples/snap/log.27Nov18.snap.compute.g++.4
Normal file
199
examples/snap/log.27Nov18.snap.compute.g++.4
Normal file
@ -0,0 +1,199 @@
|
|||||||
|
LAMMPS (20 Nov 2019)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 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 nx equal 1
|
||||||
|
variable ny equal ${nrep}
|
||||||
|
variable ny equal 1
|
||||||
|
variable nz equal ${nrep}
|
||||||
|
variable nz equal 1
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_modify map hash
|
||||||
|
lattice bcc $a
|
||||||
|
lattice bcc 2
|
||||||
|
Lattice spacing in x,y,z = 2 2 2
|
||||||
|
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||||
|
region box block 0 1 0 ${ny} 0 ${nz}
|
||||||
|
region box block 0 1 0 1 0 ${nz}
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0 0 0) to (2 2 2)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 2 box
|
||||||
|
Created 2 atoms
|
||||||
|
create_atoms CPU = 0.000610113 secs
|
||||||
|
|
||||||
|
mass * 180.88
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 123456
|
||||||
|
|
||||||
|
# choose SNA parameters
|
||||||
|
|
||||||
|
variable twojmax equal 2
|
||||||
|
variable rcutfac equal 1.0
|
||||||
|
variable rfac0 equal 0.99363
|
||||||
|
variable rmin0 equal 0
|
||||||
|
variable radelem1 equal 2.3
|
||||||
|
variable radelem2 equal 2.0
|
||||||
|
variable wj1 equal 1.0
|
||||||
|
variable wj2 equal 0.96
|
||||||
|
variable quadratic equal 0
|
||||||
|
variable bzero equal 0
|
||||||
|
variable switch equal 0
|
||||||
|
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||||
|
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||||
|
|
||||||
|
# set up dummy potential to satisfy cutoff
|
||||||
|
|
||||||
|
pair_style zero ${rcutfac}
|
||||||
|
pair_style zero 1
|
||||||
|
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_style zbl 4 ${zblcutouter}
|
||||||
|
pair_style zbl 4 4.8
|
||||||
|
pair_coeff * * ${zblz} ${zblz}
|
||||||
|
pair_coeff * * 73 ${zblz}
|
||||||
|
pair_coeff * * 73 73
|
||||||
|
|
||||||
|
# set up per-atom computes
|
||||||
|
|
||||||
|
compute b all sna/atom ${snap_options}
|
||||||
|
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||||
|
compute vb all snav/atom ${snap_options}
|
||||||
|
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||||
|
compute db all snad/atom ${snap_options}
|
||||||
|
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||||
|
|
||||||
|
# perform sums over atoms
|
||||||
|
|
||||||
|
group snapgroup1 type 1
|
||||||
|
0 atoms in group snapgroup1
|
||||||
|
group snapgroup2 type 2
|
||||||
|
2 atoms in group snapgroup2
|
||||||
|
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_30 equal c_db[2][30]
|
||||||
|
|
||||||
|
# set up compute snap generating global array
|
||||||
|
|
||||||
|
compute snap all snap ${snap_options}
|
||||||
|
compute snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||||
|
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(B_{000}^i, all i of type 2)
|
||||||
|
# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||||
|
# 5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||||
|
#
|
||||||
|
# followed by 5 counterparts from compute snap
|
||||||
|
|
||||||
|
thermo_style custom pe pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
|
||||||
|
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}
|
||||||
|
run 0
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 6.8
|
||||||
|
ghost atom cutoff = 6.8
|
||||||
|
binsize = 3.4, bins = 1 1 1
|
||||||
|
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||||
|
(1) pair zbl, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
(2) compute sna/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(3) compute snav/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(4) compute snad/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(5) compute snap, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 8.211 | 8.254 | 8.295 Mbytes
|
||||||
|
PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
|
||||||
|
322.86952 1505558.1 364182.88 381.32218 -855.04473 322.86952 1505558.1 364182.88 381.32218 -855.04473
|
||||||
|
Loop time of 2.38419e-06 on 4 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
104.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.384e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 1 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 734.5 ave 735 max 734 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 82.5 ave 177 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||||
|
FullNghs: 165 ave 330 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 660
|
||||||
|
Ave neighs/atom = 330
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
198
examples/snap/log.27Nov18.snap.compute.quadratic.g++.1
Normal file
198
examples/snap/log.27Nov18.snap.compute.quadratic.g++.1
Normal file
@ -0,0 +1,198 @@
|
|||||||
|
LAMMPS (20 Nov 2019)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 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 nx equal 1
|
||||||
|
variable ny equal ${nrep}
|
||||||
|
variable ny equal 1
|
||||||
|
variable nz equal ${nrep}
|
||||||
|
variable nz equal 1
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_modify map hash
|
||||||
|
lattice bcc $a
|
||||||
|
lattice bcc 2
|
||||||
|
Lattice spacing in x,y,z = 2 2 2
|
||||||
|
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||||
|
region box block 0 1 0 ${ny} 0 ${nz}
|
||||||
|
region box block 0 1 0 1 0 ${nz}
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0 0 0) to (2 2 2)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 2 box
|
||||||
|
Created 2 atoms
|
||||||
|
create_atoms CPU = 0.000473976 secs
|
||||||
|
|
||||||
|
mass * 180.88
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 123456
|
||||||
|
|
||||||
|
# choose SNA parameters
|
||||||
|
|
||||||
|
variable twojmax equal 2
|
||||||
|
variable rcutfac equal 1.0
|
||||||
|
variable rfac0 equal 0.99363
|
||||||
|
variable rmin0 equal 0
|
||||||
|
variable radelem1 equal 2.3
|
||||||
|
variable radelem2 equal 2.0
|
||||||
|
variable wj1 equal 1.0
|
||||||
|
variable wj2 equal 0.96
|
||||||
|
variable quadratic equal 1
|
||||||
|
variable bzero equal 0
|
||||||
|
variable switch equal 0
|
||||||
|
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||||
|
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
|
||||||
|
# set up dummy potential to satisfy cutoff
|
||||||
|
|
||||||
|
pair_style zero ${rcutfac}
|
||||||
|
pair_style zero 1
|
||||||
|
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_style zbl 4 ${zblcutouter}
|
||||||
|
pair_style zbl 4 4.8
|
||||||
|
pair_coeff * * ${zblz} ${zblz}
|
||||||
|
pair_coeff * * 73 ${zblz}
|
||||||
|
pair_coeff * * 73 73
|
||||||
|
|
||||||
|
# set up per-atom computes
|
||||||
|
|
||||||
|
compute b all sna/atom ${snap_options}
|
||||||
|
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
compute vb all snav/atom ${snap_options}
|
||||||
|
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
compute db all snad/atom ${snap_options}
|
||||||
|
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
|
||||||
|
# perform sums over atoms
|
||||||
|
|
||||||
|
group snapgroup1 type 1
|
||||||
|
0 atoms in group snapgroup1
|
||||||
|
group snapgroup2 type 2
|
||||||
|
2 atoms in group snapgroup2
|
||||||
|
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}
|
||||||
|
compute snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
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}
|
||||||
|
run 0
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 6.8
|
||||||
|
ghost atom cutoff = 6.8
|
||||||
|
binsize = 3.4, bins = 1 1 1
|
||||||
|
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||||
|
(1) pair zbl, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
(2) compute sna/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(3) compute snav/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(4) compute snad/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(5) compute snap, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 21.78 | 21.78 | 21.78 Mbytes
|
||||||
|
PotEng 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]
|
||||||
|
322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699 322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699
|
||||||
|
Loop time of 2.14577e-06 on 1 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
93.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.146e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 853 ave 853 max 853 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 330 ave 330 max 330 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 660 ave 660 max 660 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 660
|
||||||
|
Ave neighs/atom = 330
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
199
examples/snap/log.27Nov18.snap.compute.quadratic.g++.4
Normal file
199
examples/snap/log.27Nov18.snap.compute.quadratic.g++.4
Normal file
@ -0,0 +1,199 @@
|
|||||||
|
LAMMPS (20 Nov 2019)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 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 nx equal 1
|
||||||
|
variable ny equal ${nrep}
|
||||||
|
variable ny equal 1
|
||||||
|
variable nz equal ${nrep}
|
||||||
|
variable nz equal 1
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_modify map hash
|
||||||
|
lattice bcc $a
|
||||||
|
lattice bcc 2
|
||||||
|
Lattice spacing in x,y,z = 2 2 2
|
||||||
|
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||||
|
region box block 0 1 0 ${ny} 0 ${nz}
|
||||||
|
region box block 0 1 0 1 0 ${nz}
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0 0 0) to (2 2 2)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 2 box
|
||||||
|
Created 2 atoms
|
||||||
|
create_atoms CPU = 0.000118971 secs
|
||||||
|
|
||||||
|
mass * 180.88
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 123456
|
||||||
|
|
||||||
|
# choose SNA parameters
|
||||||
|
|
||||||
|
variable twojmax equal 2
|
||||||
|
variable rcutfac equal 1.0
|
||||||
|
variable rfac0 equal 0.99363
|
||||||
|
variable rmin0 equal 0
|
||||||
|
variable radelem1 equal 2.3
|
||||||
|
variable radelem2 equal 2.0
|
||||||
|
variable wj1 equal 1.0
|
||||||
|
variable wj2 equal 0.96
|
||||||
|
variable quadratic equal 1
|
||||||
|
variable bzero equal 0
|
||||||
|
variable switch equal 0
|
||||||
|
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||||
|
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
|
||||||
|
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
|
||||||
|
# set up dummy potential to satisfy cutoff
|
||||||
|
|
||||||
|
pair_style zero ${rcutfac}
|
||||||
|
pair_style zero 1
|
||||||
|
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_style zbl 4 ${zblcutouter}
|
||||||
|
pair_style zbl 4 4.8
|
||||||
|
pair_coeff * * ${zblz} ${zblz}
|
||||||
|
pair_coeff * * 73 ${zblz}
|
||||||
|
pair_coeff * * 73 73
|
||||||
|
|
||||||
|
# set up per-atom computes
|
||||||
|
|
||||||
|
compute b all sna/atom ${snap_options}
|
||||||
|
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
compute vb all snav/atom ${snap_options}
|
||||||
|
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
compute db all snad/atom ${snap_options}
|
||||||
|
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
|
||||||
|
# perform sums over atoms
|
||||||
|
|
||||||
|
group snapgroup1 type 1
|
||||||
|
0 atoms in group snapgroup1
|
||||||
|
group snapgroup2 type 2
|
||||||
|
2 atoms in group snapgroup2
|
||||||
|
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}
|
||||||
|
compute snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||||
|
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}
|
||||||
|
run 0
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 6.8
|
||||||
|
ghost atom cutoff = 6.8
|
||||||
|
binsize = 3.4, bins = 1 1 1
|
||||||
|
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||||
|
(1) pair zbl, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
(2) compute sna/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(3) compute snav/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(4) compute snad/atom, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(5) compute snap, occasional
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 19.7 | 19.74 | 19.78 Mbytes
|
||||||
|
PotEng 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]
|
||||||
|
322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699 322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699
|
||||||
|
Loop time of 2.80142e-06 on 4 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
107.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.801e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 1 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 734.5 ave 735 max 734 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 82.5 ave 177 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||||
|
FullNghs: 165 ave 330 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 660
|
||||||
|
Ave neighs/atom = 330
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -10,19 +10,7 @@
|
|||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
/* IDEAS
|
|
||||||
|
|
||||||
-DONE: Need to define a local peratom array for snad and snad on local and ghost atoms
|
|
||||||
-DONE: Reverse communicate local peratom array
|
|
||||||
-DONE: Copy peratom array into output array
|
|
||||||
-DONE: size_array_cols = nperdim (ncoeff [+quadratic])
|
|
||||||
-DONE: size_array_rows = 1 + total number of atoms + 6
|
|
||||||
-DONE: size_peratom = (3+6)*nperdim*ntypes
|
|
||||||
INCOMPLETE: Mappy from local to global
|
|
||||||
INCOMPLETE: modify->find_compute()
|
|
||||||
DONE: eliminate local peratom array for viral, replace with fdotr
|
|
||||||
|
|
||||||
*/
|
|
||||||
#include "compute_snap.h"
|
#include "compute_snap.h"
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
@ -400,18 +388,19 @@ void ComputeSnap::compute_array()
|
|||||||
|
|
||||||
// linear contributions
|
// linear contributions
|
||||||
|
|
||||||
|
int k = typeoffset_global;
|
||||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
|
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
|
||||||
snap[0][icoeff+typeoffset_global] += snaptr->blist[icoeff];
|
snap[0][k++] += snaptr->blist[icoeff];
|
||||||
|
|
||||||
// quadratic contributions
|
// quadratic contributions
|
||||||
|
|
||||||
if (quadraticflag) {
|
if (quadraticflag) {
|
||||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||||
double bveci = snaptr->blist[icoeff];
|
double bveci = snaptr->blist[icoeff];
|
||||||
snap[0][icoeff+typeoffset_global] += 0.5*bveci*bveci;
|
snap[0][k++] += 0.5*bveci*bveci;
|
||||||
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
|
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
|
||||||
double bvecj = snaptr->blist[jcoeff];
|
double bvecj = snaptr->blist[jcoeff];
|
||||||
snap[0][icoeff+typeoffset_global] += bveci*bvecj;
|
snap[0][k++] += bveci*bvecj;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user