2015-08-29 07:50:01 +08:00
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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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2016-08-24 06:17:44 +08:00
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# make certain that shake constraints are satisfied
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run 0 post no
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2015-08-29 07:50:01 +08:00
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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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