Commit 67962b15 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

a bunch refactoring changes in the python pair style and the examples 

- make all python potential classes derived from LAMMPSPairPotential
  which contains shared functionality. We currently don't check
  for supported atom types. may want to add that again later.
- keep track of skipped atom types in the C++ code.
- add test against units setting. must set self.units='...' in constructor
- make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force.
- rename potentials.py to py_pot.py
- update test runs. some small tweaks.
parent 1d48f287

examples/python/in.pair_python_coulomb

+2 −2
Original line number Diff line number Diff line
@@ -3,11 +3,11 @@ atom_style full 


read_data	data.spce



pair_style	hybrid/overlay python 12.0 coul/long 12.0

pair_style	hybrid/overlay coul/long 12.0 python 12.0

kspace_style	pppm 1.0e-6



pair_coeff	* * coul/long

pair_coeff	* * python potentials.LJCutSPCE OW NULL

pair_coeff	* * python py_pot.LJCutSPCE OW NULL



pair_modify     table 0

examples/python/in.pair_python_hybrid

+3 −3
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ mass * 1.0 
velocity	all create 3.0 87287



pair_style	hybrid lj/cut 2.5 python 2.5

pair_coeff	* * python potentials.LJCutMelt lj NULL

pair_coeff	* * python py_pot.LJCutMelt lj NULL

pair_coeff      * 2 lj/cut 1.0 1.0



neighbor	0.3 bin
@@ -31,7 +31,7 @@ clear 
read_restart    hybrid.restart



pair_style	hybrid lj/cut 2.5 python 2.5

pair_coeff	* * python potentials.LJCutMelt lj NULL

pair_coeff	* * python py_pot.LJCutMelt lj NULL

pair_coeff      * 2 lj/cut 1.0 1.0



fix		1 all nve
@@ -47,7 +47,7 @@ atom_style atomic 
read_data       hybrid.data



pair_style	hybrid lj/cut 2.5 python 2.5

pair_coeff	* * python potentials.LJCutMelt lj NULL

pair_coeff	* * python py_pot.LJCutMelt lj NULL

pair_coeff      * 2 lj/cut 1.0 1.0



neighbor	0.3 bin

examples/python/in.pair_python_melt

+3 −3
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ mass * 1.0 
velocity	all create 3.0 87287



pair_style	python 2.5

pair_coeff	* * potentials.LJCutMelt lj

pair_coeff	* * py_pot.LJCutMelt lj



neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no
@@ -30,7 +30,7 @@ clear 
read_restart    melt.restart



pair_style	python 2.5

pair_coeff	* * potentials.LJCutMelt lj

pair_coeff	* * py_pot.LJCutMelt lj



fix		1 all nve
@@ -45,7 +45,7 @@ atom_style atomic 
read_data       melt.data



pair_style	python 2.5

pair_coeff	* * potentials.LJCutMelt lj

pair_coeff	* * py_pot.LJCutMelt lj



neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no

examples/python/in.pair_python_spce

+2 −2
Original line number Diff line number Diff line
@@ -3,11 +3,11 @@ atom_style full 


read_data	data.spce



pair_style	hybrid/overlay python 12.0 coul/long 12.0

pair_style	hybrid/overlay coul/long 12.0 python 12.0

kspace_style	pppm 1.0e-6



pair_coeff	* * coul/long

pair_coeff	* * python potentials.LJCutSPCE OW NULL

pair_coeff	* * python py_pot.LJCutSPCE OW NULL



bond_style	harmonic

angle_style	harmonic

examples/python/in.pair_python_table

+3 −3
Original line number Diff line number Diff line
@@ -12,12 +12,12 @@ mass * 1.0 
velocity	all create 3.0 87287



pair_style	python 2.5

pair_coeff	* * potentials.LJCutMelt lj

pair_coeff	* * py_pot.LJCutMelt lj



# generate tabulated potential from python variant

pair_write      1 1 10000 rsq 0.01 2.5 lj_1_1.table LJ

pair_write      1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ



pair_style      table linear 10000

pair_style      table linear 2000

pair_coeff      1 1 lj_1_1.table LJ



neighbor	0.3 bin

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