git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13956 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
6
examples/USER/tally/README
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6
examples/USER/tally/README
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Examples and tests for USER-TALLY compute styles.
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The examples in this directory show where and how compute tally styles
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are equivalent to other facilities in LAMMPS and thus they can also be
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used to validate their correct function. Various columns should have
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equivalent or idential output as indicated in the input.
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9029
examples/USER/tally/data.spce
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9029
examples/USER/tally/data.spce
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File diff suppressed because it is too large
Load Diff
57
examples/USER/tally/in.force
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57
examples/USER/tally/in.force
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units real
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atom_style full
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read_data data.spce
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pair_style lj/cut/coul/long 12.0 12.0
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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fix 2 all nvt temp 300.0 300.0 100.0
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group one molecule 1 2
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# the following section shows equivalences between using the force/tally compute and other computes and thermo keywords
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# compute pairwise force between two molecules and everybody
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compute fpa one group/group all pair yes kspace no boundary no
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# tally pairwise force between two molecules and the all molecules
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compute c1 one force/tally all
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# tally the force of all with all (should be zero)
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compute c2 all force/tally all
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# collect per atom data. only reduce over the first group.
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compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
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compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
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# determine magnitude of force
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variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
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variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
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# round to 10**-10 absolute precision.
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variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
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variable all equal round(1e10*c_c2)*1e-10
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velocity all create 300 432567 dist uniform
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timestep 2.0
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# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
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thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
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thermo 10
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run 50
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63
examples/USER/tally/in.pe
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63
examples/USER/tally/in.pe
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units real
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atom_style full
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read_data data.spce
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pair_style lj/cut/coul/long 12.0 12.0
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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fix 2 all nvt temp 300.0 300.0 100.0
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group oxy type 1
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group hyd type 2
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# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
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# compute pairwise energy between all oxygen and all hydrogen
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compute epa oxy group/group hyd pair yes kspace no boundary no
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# tally pairwise energy between all oygen and all hydrogen
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compute c1 oxy pe/tally hyd
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# tally pairwise energy beween all atoms to compare with globals
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compute c2 all pe/tally all
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# collect per atom energies
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compute c3 all pe/atom pair
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# reduce over the first group only the per-atom data is storing VDW and Coulomb separately...
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compute oxy oxy reduce sum c_c1[1] c_c1[2]
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compute red all reduce sum c_c2[1] c_c2[2] c_c3
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# ... thus to get the same as compute group/group, we need to add the two
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# ... and multiply by 2.0 since compute group/group sums the pair energy, while we collect only for the first group.
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variable epa equal 2.0*(c_oxy[1]+c_oxy[2])
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# compute equivalent values to globals
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variable vdwl equal c_red[1]
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variable coul equal c_red[2]
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variable pe equal c_red[3]
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variable pair equal v_vdwl+v_coul
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variable eref equal epair-elong
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velocity all create 300 432567 dist uniform
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timestep 2.0
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# c_epa and v_epa, evdwl and v_vdwl, ecoul and v_coul, and the last 4 columns each should have identical value
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thermo_style custom step c_epa v_epa evdwl v_vdwl ecoul v_coul v_eref v_pe c_c2 v_pair
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thermo 10
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run 50
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55
examples/USER/tally/in.stress
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55
examples/USER/tally/in.stress
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@ -0,0 +1,55 @@
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units real
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atom_style full
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read_data data.spce
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pair_style lj/cut/coul/long 12.0 12.0
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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fix 2 all nvt temp 300.0 300.0 100.0
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group one molecule 1 2
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# the following section shows equivalences between using the stress/tally compute and other computes and thermo keywords
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# compute per atom stress contributions
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compute spa all stress/atom NULL pair
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compute press all pressure NULL pair
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# compute stress contributions from one group with all
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compute c1 one stress/tally all
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# collect stress contributions from all with all
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compute c2 all stress/tally all
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compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] c_spa[1] c_spa[2] c_spa[3]
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compute red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c2[1] c_c2[2] c_c2[3]
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#
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variable spa equal -(c_red[1]+c_red[2]+c_red[3])/(3.0*vol)
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variable press equal -(c_red[4]+c_red[5]+c_red[6])/(3.0*vol)
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variable one equal (c_one[1]+c_one[2]+c_one[3])/3.0
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variable ref equal (c_one[4]+c_one[5]+c_one[6])/3.0
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#velocity all create 300 432567 dist uniform
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timestep 2.0
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thermo_style custom step c_press v_spa v_press v_one v_ref
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thermo 10
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run 50
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136
examples/USER/tally/log.21Aug15.force.1
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136
examples/USER/tally/log.21Aug15.force.1
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LAMMPS (21 Aug 2015-ICMS)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style full
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3000 bonds
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reading angles ...
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1500 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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pair_style lj/cut/coul/long 12.0 12.0
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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2 = max # of special neighbors
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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1500 = # of frozen angles
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fix 2 all nvt temp 300.0 300.0 100.0
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group one molecule 1 2
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6 atoms in group one
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# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
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# compute pairwise force between two molecules and everybody
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compute fpa one group/group all pair yes kspace no boundary no
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# tally pairwise force between two molecules and the all molecules
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compute c1 one force/tally all
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# tally the force of all with all (should be zero)
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compute c2 all force/tally all
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# collect per atom data. only reduce over the first group.
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compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
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compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
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# determine magnitude of force
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variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
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variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
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# round to 10**-10 absolute precision.
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variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
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velocity all create 300 432567 dist uniform
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timestep 2.0
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# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
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thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2
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thermo 10
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run 50
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PPPM initialization ...
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G vector (1/distance) = 0.218482
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0319435
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estimated relative force accuracy = 9.61968e-05
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using double precision FFTs
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3d grid and FFT values/proc = 8000 3375
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WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
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WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
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Neighbor list info ...
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|
2 neighbor list requests
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|
update every 1 steps, delay 10 steps, check yes
|
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|
master list distance cutoff = 14
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|
ghost atom cutoff = 14
|
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|
binsize = 7 -> bins = 6 6 6
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|
Memory usage per processor = 16.7648 Mbytes
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Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2
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0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0
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||||||
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10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0
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||||||
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20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0
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||||||
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30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0
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||||||
|
40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0
|
||||||
|
50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0
|
||||||
|
|
||||||
|
Loop time of 4.11825 on 1 procs for 50 steps with 4500 atoms
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||||||
|
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
Performance: 2.098 ns/day 11.440 hours/ns 12.141 timesteps/s
|
||||||
|
|
||||||
|
MPI task timings breakdown:
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||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
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||||||
|
Pair | 3.5286 | 3.5286 | 3.5286 | 0.0 | 85.68
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||||||
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Bond | 6.1274e-05 | 6.1274e-05 | 6.1274e-05 | 0.0 | 0.00
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Kspace | 0.1937 | 0.1937 | 0.1937 | 0.0 | 4.70
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||||||
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Neigh | 0.31454 | 0.31454 | 0.31454 | 0.0 | 7.64
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||||||
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Comm | 0.01037 | 0.01037 | 0.01037 | 0.0 | 0.25
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||||||
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Output | 0.039355 | 0.039355 | 0.039355 | 0.0 | 0.96
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||||||
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Modify | 0.029273 | 0.029273 | 0.029273 | 0.0 | 0.71
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||||||
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Other | | 0.002351 | | | 0.06
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||||||
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|
||||||
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Nlocal: 4500 ave 4500 max 4500 min
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||||||
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Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
|
Nghost: 21131 ave 21131 max 21131 min
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||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
|
Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
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|
||||||
|
Total # of neighbors = 2601984
|
||||||
|
Ave neighs/atom = 578.219
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 4
|
||||||
|
Dangerous builds = 1
|
||||||
|
|
||||||
|
Total wall time: 0:00:04
|
||||||
136
examples/USER/tally/log.21Aug15.force.4
Normal file
136
examples/USER/tally/log.21Aug15.force.4
Normal file
@ -0,0 +1,136 @@
|
|||||||
|
LAMMPS (21 Aug 2015-ICMS)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
read_data data.spce
|
||||||
|
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
3000 bonds
|
||||||
|
reading angles ...
|
||||||
|
1500 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/long 12.0 12.0
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.15535 3.166
|
||||||
|
pair_coeff * 2 0.0000 0.0000
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style none
|
||||||
|
improper_style none
|
||||||
|
|
||||||
|
bond_coeff 1 1000.00 1.000
|
||||||
|
angle_coeff 1 100.0 109.47
|
||||||
|
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
|
||||||
|
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
1500 = # of frozen angles
|
||||||
|
fix 2 all nvt temp 300.0 300.0 100.0
|
||||||
|
|
||||||
|
group one molecule 1 2
|
||||||
|
6 atoms in group one
|
||||||
|
|
||||||
|
# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
|
||||||
|
|
||||||
|
# compute pairwise force between two molecules and everybody
|
||||||
|
compute fpa one group/group all pair yes kspace no boundary no
|
||||||
|
# tally pairwise force between two molecules and the all molecules
|
||||||
|
compute c1 one force/tally all
|
||||||
|
# tally the force of all with all (should be zero)
|
||||||
|
compute c2 all force/tally all
|
||||||
|
# collect per atom data. only reduce over the first group.
|
||||||
|
compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
|
||||||
|
compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
|
||||||
|
# determine magnitude of force
|
||||||
|
variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
|
||||||
|
variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
|
||||||
|
# round to 10**-10 absolute precision.
|
||||||
|
variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
|
||||||
|
|
||||||
|
velocity all create 300 432567 dist uniform
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
|
||||||
|
thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
run 50
|
||||||
|
PPPM initialization ...
|
||||||
|
G vector (1/distance) = 0.218482
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0319435
|
||||||
|
estimated relative force accuracy = 9.61968e-05
|
||||||
|
using double precision FFTs
|
||||||
|
3d grid and FFT values/proc = 3380 960
|
||||||
|
WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
|
||||||
|
WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
|
||||||
|
Neighbor list info ...
|
||||||
|
2 neighbor list requests
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7 -> bins = 6 6 6
|
||||||
|
Memory usage per processor = 8.16441 Mbytes
|
||||||
|
Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2
|
||||||
|
0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0
|
||||||
|
10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0
|
||||||
|
20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0
|
||||||
|
30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0
|
||||||
|
40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0
|
||||||
|
50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0
|
||||||
|
|
||||||
|
Loop time of 1.13658 on 4 procs for 50 steps with 4500 atoms
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
Performance: 7.602 ns/day 3.157 hours/ns 43.991 timesteps/s
|
||||||
|
|
||||||
|
MPI task timings breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.85795 | 0.89088 | 0.93636 | 3.0 | 78.38
|
||||||
|
Bond | 3.4571e-05 | 4.4644e-05 | 5.4598e-05 | 0.1 | 0.00
|
||||||
|
Kspace | 0.059847 | 0.1051 | 0.1384 | 8.9 | 9.25
|
||||||
|
Neigh | 0.085891 | 0.085954 | 0.086 | 0.0 | 7.56
|
||||||
|
Comm | 0.01758 | 0.018091 | 0.019178 | 0.5 | 1.59
|
||||||
|
Output | 0.013697 | 0.013725 | 0.013805 | 0.0 | 1.21
|
||||||
|
Modify | 0.021068 | 0.021137 | 0.021205 | 0.0 | 1.86
|
||||||
|
Other | | 0.001656 | | | 0.15
|
||||||
|
|
||||||
|
Nlocal: 1125 ave 1148 max 1097 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
Nghost: 12212.5 ave 12269 max 12162 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
Neighs: 650496 ave 675112 max 631353 min
|
||||||
|
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 2601984
|
||||||
|
Ave neighs/atom = 578.219
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 4
|
||||||
|
Dangerous builds = 1
|
||||||
|
|
||||||
|
Total wall time: 0:00:01
|
||||||
144
examples/USER/tally/log.21Aug15.pe.1
Normal file
144
examples/USER/tally/log.21Aug15.pe.1
Normal file
@ -0,0 +1,144 @@
|
|||||||
|
LAMMPS (21 Aug 2015-ICMS)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
read_data data.spce
|
||||||
|
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
3000 bonds
|
||||||
|
reading angles ...
|
||||||
|
1500 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/long 12.0 12.0
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.15535 3.166
|
||||||
|
pair_coeff * 2 0.0000 0.0000
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style none
|
||||||
|
improper_style none
|
||||||
|
|
||||||
|
bond_coeff 1 1000.00 1.000
|
||||||
|
angle_coeff 1 100.0 109.47
|
||||||
|
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
|
||||||
|
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
1500 = # of frozen angles
|
||||||
|
fix 2 all nvt temp 300.0 300.0 100.0
|
||||||
|
|
||||||
|
group oxy type 1
|
||||||
|
1500 atoms in group oxy
|
||||||
|
group hyd type 2
|
||||||
|
3000 atoms in group hyd
|
||||||
|
|
||||||
|
# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
|
||||||
|
|
||||||
|
# compute pairwise energy between all oxygen and all hydrogen
|
||||||
|
compute epa oxy group/group hyd pair yes kspace no boundary no
|
||||||
|
# tally pairwise energy between all oygen and all hydrogen
|
||||||
|
compute c1 oxy pe/tally hyd
|
||||||
|
# tally pairwise energy beween all atoms to compare with globals
|
||||||
|
compute c2 all pe/tally all
|
||||||
|
# collect per atom energies
|
||||||
|
compute c3 all pe/atom pair
|
||||||
|
# reduce over the first group only the per-atom data is storing VDW and Coulomb separately...
|
||||||
|
compute oxy oxy reduce sum c_c1[1] c_c1[2]
|
||||||
|
compute red all reduce sum c_c2[1] c_c2[2] c_c3
|
||||||
|
# ... thus to get the same as compute group/group, we need to add the two
|
||||||
|
# ... and multiply by 2.0 since compute group/group sums the pair energy, while we collect only for the first group.
|
||||||
|
variable epa equal 2.0*(c_oxy[1]+c_oxy[2])
|
||||||
|
# compute equivalent values to globals
|
||||||
|
variable vdwl equal c_red[1]
|
||||||
|
variable coul equal c_red[2]
|
||||||
|
variable pe equal c_red[3]
|
||||||
|
variable pair equal v_vdwl+v_coul
|
||||||
|
variable eref equal epair-elong
|
||||||
|
|
||||||
|
velocity all create 300 432567 dist uniform
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
# c_epa and v_epa, evdwl and v_vdwl, ecoul and v_coul, and the last 4 columns each should have identical value
|
||||||
|
thermo_style custom step c_epa v_epa evdwl v_vdwl ecoul v_coul v_eref v_pe c_c2 v_pair
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
run 50
|
||||||
|
PPPM initialization ...
|
||||||
|
G vector (1/distance) = 0.218482
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0319435
|
||||||
|
estimated relative force accuracy = 9.61968e-05
|
||||||
|
using double precision FFTs
|
||||||
|
3d grid and FFT values/proc = 8000 3375
|
||||||
|
WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
|
||||||
|
WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
|
||||||
|
Neighbor list info ...
|
||||||
|
2 neighbor list requests
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7 -> bins = 6 6 6
|
||||||
|
Memory usage per processor = 17.381 Mbytes
|
||||||
|
Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair
|
||||||
|
0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827
|
||||||
|
10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972
|
||||||
|
20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572
|
||||||
|
30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165
|
||||||
|
40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345
|
||||||
|
50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911
|
||||||
|
|
||||||
|
Loop time of 4.31105 on 1 procs for 50 steps with 4500 atoms
|
||||||
|
100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
Performance: 2.004 ns/day 11.975 hours/ns 11.598 timesteps/s
|
||||||
|
|
||||||
|
MPI task timings breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.5071 | 3.5071 | 3.5071 | 0.0 | 81.35
|
||||||
|
Bond | 0.00025034 | 0.00025034 | 0.00025034 | 0.0 | 0.01
|
||||||
|
Kspace | 0.19991 | 0.19991 | 0.19991 | 0.0 | 4.64
|
||||||
|
Neigh | 0.31459 | 0.31459 | 0.31459 | 0.0 | 7.30
|
||||||
|
Comm | 0.010338 | 0.010338 | 0.010338 | 0.0 | 0.24
|
||||||
|
Output | 0.24722 | 0.24722 | 0.24722 | 0.0 | 5.73
|
||||||
|
Modify | 0.029466 | 0.029466 | 0.029466 | 0.0 | 0.68
|
||||||
|
Other | | 0.002182 | | | 0.05
|
||||||
|
|
||||||
|
Nlocal: 4500 ave 4500 max 4500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 21131 ave 21131 max 21131 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2601984
|
||||||
|
Ave neighs/atom = 578.219
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 4
|
||||||
|
Dangerous builds = 1
|
||||||
|
|
||||||
|
Total wall time: 0:00:04
|
||||||
144
examples/USER/tally/log.21Aug15.pe.4
Normal file
144
examples/USER/tally/log.21Aug15.pe.4
Normal file
@ -0,0 +1,144 @@
|
|||||||
|
LAMMPS (21 Aug 2015-ICMS)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
read_data data.spce
|
||||||
|
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
3000 bonds
|
||||||
|
reading angles ...
|
||||||
|
1500 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/long 12.0 12.0
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.15535 3.166
|
||||||
|
pair_coeff * 2 0.0000 0.0000
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style none
|
||||||
|
improper_style none
|
||||||
|
|
||||||
|
bond_coeff 1 1000.00 1.000
|
||||||
|
angle_coeff 1 100.0 109.47
|
||||||
|
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
|
||||||
|
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
1500 = # of frozen angles
|
||||||
|
fix 2 all nvt temp 300.0 300.0 100.0
|
||||||
|
|
||||||
|
group oxy type 1
|
||||||
|
1500 atoms in group oxy
|
||||||
|
group hyd type 2
|
||||||
|
3000 atoms in group hyd
|
||||||
|
|
||||||
|
# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
|
||||||
|
|
||||||
|
# compute pairwise energy between all oxygen and all hydrogen
|
||||||
|
compute epa oxy group/group hyd pair yes kspace no boundary no
|
||||||
|
# tally pairwise energy between all oygen and all hydrogen
|
||||||
|
compute c1 oxy pe/tally hyd
|
||||||
|
# tally pairwise energy beween all atoms to compare with globals
|
||||||
|
compute c2 all pe/tally all
|
||||||
|
# collect per atom energies
|
||||||
|
compute c3 all pe/atom pair
|
||||||
|
# reduce over the first group only the per-atom data is storing VDW and Coulomb separately...
|
||||||
|
compute oxy oxy reduce sum c_c1[1] c_c1[2]
|
||||||
|
compute red all reduce sum c_c2[1] c_c2[2] c_c3
|
||||||
|
# ... thus to get the same as compute group/group, we need to add the two
|
||||||
|
# ... and multiply by 2.0 since compute group/group sums the pair energy, while we collect only for the first group.
|
||||||
|
variable epa equal 2.0*(c_oxy[1]+c_oxy[2])
|
||||||
|
# compute equivalent values to globals
|
||||||
|
variable vdwl equal c_red[1]
|
||||||
|
variable coul equal c_red[2]
|
||||||
|
variable pe equal c_red[3]
|
||||||
|
variable pair equal v_vdwl+v_coul
|
||||||
|
variable eref equal epair-elong
|
||||||
|
|
||||||
|
velocity all create 300 432567 dist uniform
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
# c_epa and v_epa, evdwl and v_vdwl, ecoul and v_coul, and the last 4 columns each should have identical value
|
||||||
|
thermo_style custom step c_epa v_epa evdwl v_vdwl ecoul v_coul v_eref v_pe c_c2 v_pair
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
run 50
|
||||||
|
PPPM initialization ...
|
||||||
|
G vector (1/distance) = 0.218482
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0319435
|
||||||
|
estimated relative force accuracy = 9.61968e-05
|
||||||
|
using double precision FFTs
|
||||||
|
3d grid and FFT values/proc = 3380 960
|
||||||
|
WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
|
||||||
|
WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
|
||||||
|
Neighbor list info ...
|
||||||
|
2 neighbor list requests
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7 -> bins = 6 6 6
|
||||||
|
Memory usage per processor = 8.44413 Mbytes
|
||||||
|
Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair
|
||||||
|
0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827
|
||||||
|
10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972
|
||||||
|
20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572
|
||||||
|
30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165
|
||||||
|
40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345
|
||||||
|
50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911
|
||||||
|
|
||||||
|
Loop time of 1.20533 on 4 procs for 50 steps with 4500 atoms
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
Performance: 7.168 ns/day 3.348 hours/ns 41.482 timesteps/s
|
||||||
|
|
||||||
|
MPI task timings breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.87053 | 0.90325 | 0.94364 | 2.8 | 74.94
|
||||||
|
Bond | 0.00015402 | 0.00018191 | 0.00020909 | 0.2 | 0.02
|
||||||
|
Kspace | 0.061657 | 0.10164 | 0.13394 | 8.4 | 8.43
|
||||||
|
Neigh | 0.088292 | 0.088332 | 0.088373 | 0.0 | 7.33
|
||||||
|
Comm | 0.017319 | 0.017806 | 0.018291 | 0.4 | 1.48
|
||||||
|
Output | 0.07067 | 0.070706 | 0.070813 | 0.0 | 5.87
|
||||||
|
Modify | 0.021655 | 0.021694 | 0.02173 | 0.0 | 1.80
|
||||||
|
Other | | 0.001719 | | | 0.14
|
||||||
|
|
||||||
|
Nlocal: 1125 ave 1148 max 1097 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
Nghost: 12212.5 ave 12269 max 12162 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
Neighs: 650496 ave 675112 max 631353 min
|
||||||
|
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 2601984
|
||||||
|
Ave neighs/atom = 578.219
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 4
|
||||||
|
Dangerous builds = 1
|
||||||
|
|
||||||
|
Total wall time: 0:00:01
|
||||||
135
examples/USER/tally/log.21Aug15.stress.1
Normal file
135
examples/USER/tally/log.21Aug15.stress.1
Normal file
@ -0,0 +1,135 @@
|
|||||||
|
LAMMPS (21 Aug 2015-ICMS)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
read_data data.spce
|
||||||
|
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
3000 bonds
|
||||||
|
reading angles ...
|
||||||
|
1500 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/long 12.0 12.0
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.15535 3.166
|
||||||
|
pair_coeff * 2 0.0000 0.0000
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style none
|
||||||
|
improper_style none
|
||||||
|
|
||||||
|
bond_coeff 1 1000.00 1.000
|
||||||
|
angle_coeff 1 100.0 109.47
|
||||||
|
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
|
||||||
|
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
1500 = # of frozen angles
|
||||||
|
fix 2 all nvt temp 300.0 300.0 100.0
|
||||||
|
|
||||||
|
group one molecule 1 2
|
||||||
|
6 atoms in group one
|
||||||
|
|
||||||
|
# the following section shows equivalences between using the stress/tally compute and other computes and thermo keywords
|
||||||
|
|
||||||
|
# compute per atom stress contributions
|
||||||
|
compute spa all stress/atom NULL pair
|
||||||
|
compute press all pressure NULL pair
|
||||||
|
# compute stress contributions from one group with all
|
||||||
|
compute c1 one stress/tally all
|
||||||
|
# collect stress contributions from all with all
|
||||||
|
compute c2 all stress/tally all
|
||||||
|
compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] c_spa[1] c_spa[2] c_spa[3]
|
||||||
|
compute red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c2[1] c_c2[2] c_c2[3]
|
||||||
|
#
|
||||||
|
variable spa equal -(c_red[1]+c_red[2]+c_red[3])/(3.0*vol)
|
||||||
|
variable press equal -(c_red[4]+c_red[5]+c_red[6])/(3.0*vol)
|
||||||
|
variable one equal (c_one[1]+c_one[2]+c_one[3])/3.0
|
||||||
|
variable ref equal (c_one[4]+c_one[5]+c_one[6])/3.0
|
||||||
|
|
||||||
|
#velocity all create 300 432567 dist uniform
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
thermo_style custom step c_press v_spa v_press v_one v_ref
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
run 50
|
||||||
|
PPPM initialization ...
|
||||||
|
G vector (1/distance) = 0.218482
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0319435
|
||||||
|
estimated relative force accuracy = 9.61968e-05
|
||||||
|
using double precision FFTs
|
||||||
|
3d grid and FFT values/proc = 8000 3375
|
||||||
|
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
|
||||||
|
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
|
||||||
|
Neighbor list info ...
|
||||||
|
1 neighbor list requests
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7 -> bins = 6 6 6
|
||||||
|
Memory usage per processor = 24.631 Mbytes
|
||||||
|
Step press spa press one ref
|
||||||
|
0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6
|
||||||
|
10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3
|
||||||
|
20 23338.149 23338.149 23338.149 -2034283 -2034283
|
||||||
|
30 25946.4 25946.4 25946.4 -2002817 -2002817
|
||||||
|
40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5
|
||||||
|
50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3
|
||||||
|
|
||||||
|
Loop time of 4.15609 on 1 procs for 50 steps with 4500 atoms
|
||||||
|
100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
Performance: 2.079 ns/day 11.545 hours/ns 12.031 timesteps/s
|
||||||
|
|
||||||
|
MPI task timings breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.6444 | 3.6444 | 3.6444 | 0.0 | 87.69
|
||||||
|
Bond | 0.0016105 | 0.0016105 | 0.0016105 | 0.0 | 0.04
|
||||||
|
Kspace | 0.22345 | 0.22345 | 0.22345 | 0.0 | 5.38
|
||||||
|
Neigh | 0.23588 | 0.23588 | 0.23588 | 0.0 | 5.68
|
||||||
|
Comm | 0.010035 | 0.010035 | 0.010035 | 0.0 | 0.24
|
||||||
|
Output | 0.0084085 | 0.0084085 | 0.0084085 | 0.0 | 0.20
|
||||||
|
Modify | 0.029978 | 0.029978 | 0.029978 | 0.0 | 0.72
|
||||||
|
Other | | 0.002368 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 4500 ave 4500 max 4500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 21226 ave 21226 max 21226 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2.60175e+06 ave 2.60175e+06 max 2.60175e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2601750
|
||||||
|
Ave neighs/atom = 578.167
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:04
|
||||||
135
examples/USER/tally/log.21Aug15.stress.4
Normal file
135
examples/USER/tally/log.21Aug15.stress.4
Normal file
@ -0,0 +1,135 @@
|
|||||||
|
LAMMPS (21 Aug 2015-ICMS)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
read_data data.spce
|
||||||
|
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
3000 bonds
|
||||||
|
reading angles ...
|
||||||
|
1500 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
1 = max # of 1-4 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/long 12.0 12.0
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.15535 3.166
|
||||||
|
pair_coeff * 2 0.0000 0.0000
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style none
|
||||||
|
improper_style none
|
||||||
|
|
||||||
|
bond_coeff 1 1000.00 1.000
|
||||||
|
angle_coeff 1 100.0 109.47
|
||||||
|
|
||||||
|
special_bonds lj/coul 0.0 0.0 1.0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
1 = max # of 1-3 neighbors
|
||||||
|
2 = max # of special neighbors
|
||||||
|
|
||||||
|
neighbor 2.0 bin
|
||||||
|
|
||||||
|
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
1500 = # of frozen angles
|
||||||
|
fix 2 all nvt temp 300.0 300.0 100.0
|
||||||
|
|
||||||
|
group one molecule 1 2
|
||||||
|
6 atoms in group one
|
||||||
|
|
||||||
|
# the following section shows equivalences between using the stress/tally compute and other computes and thermo keywords
|
||||||
|
|
||||||
|
# compute per atom stress contributions
|
||||||
|
compute spa all stress/atom NULL pair
|
||||||
|
compute press all pressure NULL pair
|
||||||
|
# compute stress contributions from one group with all
|
||||||
|
compute c1 one stress/tally all
|
||||||
|
# collect stress contributions from all with all
|
||||||
|
compute c2 all stress/tally all
|
||||||
|
compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] c_spa[1] c_spa[2] c_spa[3]
|
||||||
|
compute red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c2[1] c_c2[2] c_c2[3]
|
||||||
|
#
|
||||||
|
variable spa equal -(c_red[1]+c_red[2]+c_red[3])/(3.0*vol)
|
||||||
|
variable press equal -(c_red[4]+c_red[5]+c_red[6])/(3.0*vol)
|
||||||
|
variable one equal (c_one[1]+c_one[2]+c_one[3])/3.0
|
||||||
|
variable ref equal (c_one[4]+c_one[5]+c_one[6])/3.0
|
||||||
|
|
||||||
|
#velocity all create 300 432567 dist uniform
|
||||||
|
|
||||||
|
timestep 2.0
|
||||||
|
|
||||||
|
thermo_style custom step c_press v_spa v_press v_one v_ref
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
run 50
|
||||||
|
PPPM initialization ...
|
||||||
|
G vector (1/distance) = 0.218482
|
||||||
|
grid = 15 15 15
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0319435
|
||||||
|
estimated relative force accuracy = 9.61968e-05
|
||||||
|
using double precision FFTs
|
||||||
|
3d grid and FFT values/proc = 3380 960
|
||||||
|
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
|
||||||
|
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
|
||||||
|
Neighbor list info ...
|
||||||
|
1 neighbor list requests
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7 -> bins = 6 6 6
|
||||||
|
Memory usage per processor = 12.0691 Mbytes
|
||||||
|
Step press spa press one ref
|
||||||
|
0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6
|
||||||
|
10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3
|
||||||
|
20 23338.149 23338.149 23338.149 -2034283 -2034283
|
||||||
|
30 25946.4 25946.4 25946.4 -2002817 -2002817
|
||||||
|
40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5
|
||||||
|
50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3
|
||||||
|
|
||||||
|
Loop time of 1.17266 on 4 procs for 50 steps with 4500 atoms
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
Performance: 7.368 ns/day 3.257 hours/ns 42.638 timesteps/s
|
||||||
|
|
||||||
|
MPI task timings breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.89832 | 0.93222 | 0.98611 | 3.4 | 79.50
|
||||||
|
Bond | 0.00081754 | 0.00096095 | 0.0011327 | 0.4 | 0.08
|
||||||
|
Kspace | 0.068058 | 0.12154 | 0.15522 | 9.4 | 10.36
|
||||||
|
Neigh | 0.065756 | 0.065785 | 0.065824 | 0.0 | 5.61
|
||||||
|
Comm | 0.017489 | 0.017982 | 0.018623 | 0.4 | 1.53
|
||||||
|
Output | 0.010985 | 0.011017 | 0.011111 | 0.1 | 0.94
|
||||||
|
Modify | 0.021429 | 0.021491 | 0.021551 | 0.0 | 1.83
|
||||||
|
Other | | 0.001671 | | | 0.14
|
||||||
|
|
||||||
|
Nlocal: 1125 ave 1154 max 1092 min
|
||||||
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||||
|
Nghost: 12263.5 ave 12300 max 12219 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||||
|
Neighs: 650438 ave 678786 max 626279 min
|
||||||
|
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 2601750
|
||||||
|
Ave neighs/atom = 578.167
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:01
|
||||||
Reference in New Issue
Block a user