forked from lijiext/lammps
Merge branch 'soft_class2_potentials' of https://github.com/evoyiatzis/lammps into combined-user-fep-soft-updates
This commit is contained in:
Axel Kohlmeyer
commit
536e34974a
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,57 @@
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# LAMMPS atomistic input script
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||||
|
||||
echo screen
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units real
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atom_style full
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pair_style hybrid lj/class2/coul/long 9.5 lj/class2/coul/long/soft 2 0.5 0.5 9.5
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bond_style class2
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angle_style class2
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||||
dihedral_style class2
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||||
improper_style class2
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||||
pair_modify mix sixthpower tail yes
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||||
special_bonds lj/coul 0 0 1
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||||
|
||||
read_data data.init_conf_without_heptane
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||||
|
||||
pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 0.0
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||||
pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 0.0
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||||
pair_coeff 3 6 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0
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||||
pair_coeff 4 6 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
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||||
pair_coeff 5 6 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0
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||||
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||||
pair_coeff 1 7 lj/class2/coul/long/soft 0.054 4.01 0.0
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||||
pair_coeff 2 7 lj/class2/coul/long/soft 0.054 4.01 0.0
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||||
pair_coeff 3 7 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0
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||||
pair_coeff 4 7 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
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pair_coeff 5 7 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0
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||||
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||||
pair_coeff 1 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
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||||
pair_coeff 2 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
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||||
pair_coeff 3 8 lj/class2/coul/long/soft 0.06151694 3.31892497 0.0
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pair_coeff 4 8 lj/class2/coul/long/soft 0.02 2.995 0.0
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||||
pair_coeff 5 8 lj/class2/coul/long/soft 0.00158519 2.66932028 0.0
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timestep 1.0
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kspace_style pppm 1.0e-5
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||||
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variable lambda equal ramp(0.0,1.0)
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variable q1 equal -0.1590*v_lambda
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variable q2 equal -0.1060*v_lambda
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variable q3 equal 0.0530*v_lambda
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|
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fix ADAPT all adapt/fep 10 &
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pair lj/class2/coul/long/soft lambda 1*5 6*8 v_lambda &
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atom charge 6 v_q1 &
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atom charge 7 v_q2 &
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atom charge 8 v_q3 &
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after yes
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thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
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thermo_modify line one
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thermo 100
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fix 1 all nvt temp 300 300 100
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run 100000
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||||
|
||||
write_data data.after_heptane_insertion
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||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,57 @@
|
|||
# LAMMPS atomistic input script
|
||||
|
||||
echo screen
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style hybrid lj/class2/coul/long 9.5 lj/class2/coul/long/soft 2 0.5 0.5 9.5
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bond_style class2
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||||
angle_style class2
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dihedral_style class2
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improper_style class2
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pair_modify mix sixthpower tail yes
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special_bonds lj/coul 0 0 1
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read_data data.init_conf_with_heptane
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|
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pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 1.0
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pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 1.0
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||||
pair_coeff 3 6 lj/class2/coul/long/soft 0.10615754 3.80912744 1.0
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pair_coeff 4 6 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
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||||
pair_coeff 5 6 lj/class2/coul/long/soft 0.00108740 3.57275476 1.0
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||||
|
||||
pair_coeff 1 7 lj/class2/coul/long/soft 0.054 4.01 1.0
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||||
pair_coeff 2 7 lj/class2/coul/long/soft 0.054 4.01 1.0
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||||
pair_coeff 3 7 lj/class2/coul/long/soft 0.10615754 3.80912744 1.0
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pair_coeff 4 7 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
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pair_coeff 5 7 lj/class2/coul/long/soft 0.00108740 3.57275476 1.0
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||||
|
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pair_coeff 1 8 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
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pair_coeff 2 8 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
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pair_coeff 3 8 lj/class2/coul/long/soft 0.06151694 3.31892497 1.0
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pair_coeff 4 8 lj/class2/coul/long/soft 0.02 2.995 1.0
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pair_coeff 5 8 lj/class2/coul/long/soft 0.00158519 2.66932028 1.0
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||||
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timestep 1.0
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||||
kspace_style pppm 1.0e-5
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||||
|
||||
variable lambda equal ramp(1.0,0.0)
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variable q1 equal -0.1590*v_lambda
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variable q2 equal -0.1060*v_lambda
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variable q3 equal 0.0530*v_lambda
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||||
|
||||
fix ADAPT all adapt/fep 10 &
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pair lj/class2/coul/long/soft lambda 1*5 6*8 v_lambda &
|
||||
atom charge 6 v_q1 &
|
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atom charge 7 v_q2 &
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||||
atom charge 8 v_q3 &
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after yes
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||||
|
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thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
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||||
thermo_modify line one
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thermo 100
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||||
|
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fix 1 all nvt temp 300 300 100
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run 100000
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write_data data.after_heptane_deletion
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File diff suppressed because it is too large
Load Diff
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@ -9,3 +9,6 @@ compute fep examples
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* `CC-CO` -- free energy difference of transforming ethane into
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methanol, in water (more complex). FEP, TI and BAR methods.
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* 'C7inEthanol' -- insertion / deletion of a hexane molecule in ethanol.
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The hexane is described by the lj/class2/coul/long/soft potential.
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@ -50,4 +50,10 @@ action pair_morse_soft.cpp
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action pair_morse_soft.h
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action pair_tip4p_long_soft.cpp pppm_tip4p.cpp
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action pair_tip4p_long_soft.h pppm_tip4p.cpp
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action pair_lj_class2_soft.cpp
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action pair_lj_class2_soft.h
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action pair_lj_class2_coul_cut_soft.cpp
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action pair_lj_class2_coul_cut_soft.h
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action pair_lj_class2_coul_long_soft.cpp pppm.cpp
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action pair_lj_class2_coul_long_soft.h pppm.cpp
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@ -16,3 +16,7 @@ Pair style morse/soft was contributed by Stefan Paquay, s.paquay at tue.nl
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Applied Physics/Theory of Polymers and Soft Matter,
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Eindhoven University of Technology (TU/e), The Netherlands
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Contact him in case of problems with this pair style.
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Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at
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Technical University of Darmstadt (e.voyiatzis at theo.chemie.tu-darmstadt.de)
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Contact him in case of problems with these pair styles.
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|
|
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@ -0,0 +1,520 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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||||
Steve Plimpton, sjplimp@sandia.gov
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||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
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||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
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||||
the GNU General Public License.
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||||
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||||
See the README file in the top-level LAMMPS directory.
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||||
------------------------------------------------------------------------- */
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||||
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||||
#include <cmath>
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||||
#include <cstdio>
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#include <cstdlib>
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#include <cstring>
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#include "pair_lj_class2_coul_cut_soft.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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||||
/* ---------------------------------------------------------------------- */
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||||
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PairLJClass2CoulCutSoft::PairLJClass2CoulCutSoft(LAMMPS *lmp) : Pair(lmp)
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{
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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PairLJClass2CoulCutSoft::~PairLJClass2CoulCutSoft()
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{
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if (!copymode) {
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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||||
memory->destroy(cut_lj);
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memory->destroy(cut_ljsq);
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||||
memory->destroy(cut_coul);
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memory->destroy(cut_coulsq);
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memory->destroy(epsilon);
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memory->destroy(sigma);
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memory->destroy(lambda);
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memory->destroy(lj1);
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memory->destroy(lj2);
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memory->destroy(lj3);
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memory->destroy(lj4);
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memory->destroy(offset);
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||||
}
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||||
}
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}
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||||
/* ---------------------------------------------------------------------- */
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||||
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void PairLJClass2CoulCutSoft::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double rsq,forcecoul,forcelj;
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double factor_coul,factor_lj;
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double denc, denlj, r4sig6;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = ecoul = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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double *q = atom->q;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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qtmp = q[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_lj = special_lj[sbmask(j)];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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|
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
if (rsq < cut_coulsq[itype][jtype]) {
|
||||
denc = sqrt(lj4[itype][jtype] + rsq);
|
||||
forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
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||||
} else forcecoul = 0.0;
|
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|
||||
if (rsq < cut_ljsq[itype][jtype]) {
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||||
denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
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||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2));
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||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = factor_coul*forcecoul + factor_lj*forcelj;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq[itype][jtype])
|
||||
ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
|
||||
else ecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
|
||||
evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
|
||||
memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
|
||||
memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lambda,n+1,n+1,"pair:lambda");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
nlambda = force->numeric(FLERR,arg[0]);
|
||||
alphalj = force->numeric(FLERR,arg[1]);
|
||||
alphac = force->numeric(FLERR,arg[2]);
|
||||
|
||||
cut_lj_global = force->numeric(FLERR,arg[3]);
|
||||
if (narg == 4) cut_coul_global = cut_lj_global;
|
||||
else cut_coul_global = force->numeric(FLERR,arg[4]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) {
|
||||
cut_lj[i][j] = cut_lj_global;
|
||||
cut_coul[i][j] = cut_coul_global;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 5 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double epsilon_one = force->numeric(FLERR,arg[2]);
|
||||
double sigma_one = force->numeric(FLERR,arg[3]);
|
||||
double lambda_one = force->numeric(FLERR,arg[4]);
|
||||
if (sigma_one <= 0.0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
double cut_coul_one = cut_coul_global;
|
||||
if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]);
|
||||
if (narg == 7) cut_coul_one = force->numeric(FLERR,arg[6]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
cut_lj[i][j] = cut_lj_one;
|
||||
lambda[i][j] = lambda_one;
|
||||
cut_coul[i][j] = cut_coul_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Pair style lj/class2/coul/cut/soft requires atom attribute q");
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2CoulCutSoft::init_one(int i, int j)
|
||||
{
|
||||
// always mix epsilon,sigma via sixthpower rules
|
||||
// mix distance via user-defined rule
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
|
||||
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
|
||||
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
|
||||
sigma[i][j] =
|
||||
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
|
||||
if (lambda[i][i] != lambda[j][j])
|
||||
error->all(FLERR,"Pair lj/class2/coul/cut/soft different lambda values in mix");
|
||||
lambda[i][j] = lambda[i][i];
|
||||
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
|
||||
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
|
||||
}
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];
|
||||
|
||||
lj1[i][j] = pow(lambda[i][j], nlambda);
|
||||
lj2[i][j] = pow(sigma[i][j], 6.0);
|
||||
lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
|
||||
lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
|
||||
|
||||
if (offset_flag && (cut_lj[i][j] > 0.0)) {
|
||||
double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0);
|
||||
offset[i][j] = lj1[i][j] * epsilon[i][j] * (2.0*pow(denlj,-1.5) - 3.0*pow(denlj,-1.0));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
epsilon[j][i] = epsilon[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
lambda[j][i] = lambda[i][j];
|
||||
cut_ljsq[j][i] = cut_ljsq[i][j];
|
||||
cut_coulsq[j][i] = cut_coulsq[i][j];
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// compute I,J contribution to long-range tail correction
|
||||
// count total # of atoms of type I and J via Allreduce
|
||||
|
||||
if (tail_flag) {
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double count[2],all[2];
|
||||
count[0] = count[1] = 0.0;
|
||||
for (int k = 0; k < nlocal; k++) {
|
||||
if (type[k] == i) count[0] += 1.0;
|
||||
if (type[k] == j) count[1] += 1.0;
|
||||
}
|
||||
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
|
||||
double sig6 = sig3*sig3;
|
||||
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
|
||||
double rc6 = rc3*rc3;
|
||||
// the tail and pressure corrections are not exact but approximate
|
||||
etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
|
||||
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
|
||||
ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
|
||||
sig6 * (sig3 - 2.0*rc3) / rc6;
|
||||
}
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||
fwrite(&lambda[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
fread(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||
fread(&lambda[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_coul[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&nlambda,sizeof(double),1,fp);
|
||||
fwrite(&alphalj,sizeof(double),1,fp);
|
||||
fwrite(&alphac,sizeof(double),1,fp);
|
||||
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
fwrite(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&nlambda,sizeof(double),1,fp);
|
||||
fread(&alphalj,sizeof(double),1,fp);
|
||||
fread(&alphac,sizeof(double),1,fp);
|
||||
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
fread(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
|
||||
|
||||
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulCutSoft::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
|
||||
lambda[i][j],cut_lj[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2CoulCutSoft::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double forcecoul,forcelj,phicoul,philj;
|
||||
double denc, denlj, r4sig6;
|
||||
|
||||
if (rsq < cut_coulsq[itype][jtype]) {
|
||||
denc = sqrt(lj4[itype][jtype] + rsq);
|
||||
forcecoul = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] /
|
||||
(denc*denc*denc);
|
||||
} else forcecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj));
|
||||
} else forcelj = 0.0;
|
||||
fforce = factor_coul*forcecoul + factor_lj*forcelj;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq[itype][jtype]) {
|
||||
phicoul = force->qqrd2e *lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
|
||||
eng += factor_coul*phicoul;
|
||||
}
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
philj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - offset[itype][jtype];
|
||||
eng += factor_lj*philj;
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJClass2CoulCutSoft::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 0;
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
||||
if (strcmp(str,"lambda") == 0) return (void *) lambda;
|
||||
return NULL;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,81 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/class2/coul/cut/soft,PairLJClass2CoulCutSoft)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CLASS2_COUL_CUT_SOFT_H
|
||||
#define LMP_PAIR_LJ_CLASS2_COUL_CUT_SOFT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJClass2CoulCutSoft : public Pair {
|
||||
public:
|
||||
PairLJClass2CoulCutSoft(class LAMMPS *);
|
||||
virtual ~PairLJClass2CoulCutSoft();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
virtual double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_lj_global,cut_coul_global;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double **cut_coul,**cut_coulsq;
|
||||
double **epsilon,**sigma, **lambda;
|
||||
double nlambda, alphalj, alphac;
|
||||
double **lj1,**lj2,**lj3,**lj4,**offset;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style lj/class2/coul/cut/soft requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
E: Pair lj/class2/coul/cut/soft different lambda values in mix
|
||||
|
||||
The value of lambda has to be the same for I J pairs.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,543 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cmath>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "pair_lj_class2_coul_long_soft.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "kspace.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJClass2CoulLongSoft::PairLJClass2CoulLongSoft(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
ewaldflag = pppmflag = 1;
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJClass2CoulLongSoft::~PairLJClass2CoulLongSoft()
|
||||
{
|
||||
if (!copymode) {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lambda);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double fraction;
|
||||
double rsq,r,forcecoul,forcelj;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
double factor_coul,factor_lj;
|
||||
double denc, denlj, r4sig6;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_coul = force->special_coul;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
denc = sqrt(lj4[itype][jtype] + rsq);
|
||||
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2));
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = forcecoul + factor_lj*forcelj;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq) {
|
||||
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
|
||||
ecoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lambda,n+1,n+1,"pair:lambda");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
nlambda = force->numeric(FLERR,arg[0]);
|
||||
alphalj = force->numeric(FLERR,arg[1]);
|
||||
alphac = force->numeric(FLERR,arg[2]);
|
||||
|
||||
cut_lj_global = force->numeric(FLERR,arg[3]);
|
||||
if (narg == 4) cut_coul = cut_lj_global;
|
||||
else cut_coul = force->numeric(FLERR,arg[4]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 5 || narg > 6)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double epsilon_one = force->numeric(FLERR,arg[2]);
|
||||
double sigma_one = force->numeric(FLERR,arg[3]);
|
||||
double lambda_one = force->numeric(FLERR,arg[4]);
|
||||
if (sigma_one <= 0.0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
lambda[i][j] = lambda_one;
|
||||
cut_lj[i][j] = cut_lj_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,
|
||||
"Pair style lj/class2/coul/long/soft requires atom attribute q");
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
|
||||
cut_coulsq = cut_coul * cut_coul;
|
||||
|
||||
// insure use of KSpace long-range solver, set g_ewald
|
||||
|
||||
if (force->kspace == NULL)
|
||||
error->all(FLERR,"Pair style requires a KSpace style");
|
||||
g_ewald = force->kspace->g_ewald;
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2CoulLongSoft::init_one(int i, int j)
|
||||
{
|
||||
// always mix epsilon,sigma via sixthpower rules
|
||||
// mix distance via user-defined rule
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
|
||||
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
|
||||
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
|
||||
sigma[i][j] =
|
||||
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
|
||||
if (lambda[i][i] != lambda[j][j])
|
||||
error->all(FLERR,"Pair lj/class2/coul/long/soft different lambda values in mix");
|
||||
lambda[i][j] = lambda[i][i];
|
||||
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
|
||||
}
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
|
||||
lj1[i][j] = pow(lambda[i][j], nlambda);
|
||||
lj2[i][j] = pow(sigma[i][j], 6.0);
|
||||
lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
|
||||
lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
|
||||
|
||||
if (offset_flag && (cut_lj[i][j] > 0.0)) {
|
||||
double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0);
|
||||
offset[i][j] = epsilon[i][j] * (2.0*pow(denlj,-1.5) - 3.0*pow(denlj,-1.0));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
epsilon[j][i] = epsilon[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
lambda[j][i] = lambda[i][j];
|
||||
cut_ljsq[j][i] = cut_ljsq[i][j];
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// compute I,J contribution to long-range tail correction
|
||||
// count total # of atoms of type I and J via Allreduce
|
||||
|
||||
if (tail_flag) {
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double count[2],all[2];
|
||||
count[0] = count[1] = 0.0;
|
||||
for (int k = 0; k < nlocal; k++) {
|
||||
if (type[k] == i) count[0] += 1.0;
|
||||
if (type[k] == j) count[1] += 1.0;
|
||||
}
|
||||
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
|
||||
double sig6 = sig3*sig3;
|
||||
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
|
||||
double rc6 = rc3*rc3;
|
||||
etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
|
||||
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
|
||||
ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
|
||||
sig6 * (sig3 - 2.0*rc3) / rc6;
|
||||
}
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||
fwrite(&lambda[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
fread(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||
fread(&lambda[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&nlambda,sizeof(double),1,fp);
|
||||
fwrite(&alphalj,sizeof(double),1,fp);
|
||||
fwrite(&alphac,sizeof(double),1,fp);
|
||||
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
fwrite(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&nlambda,sizeof(double),1,fp);
|
||||
fread(&alphalj,sizeof(double),1,fp);
|
||||
fread(&alphac,sizeof(double),1,fp);
|
||||
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
fread(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
|
||||
|
||||
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongSoft::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
|
||||
lambda[i][j],cut_lj[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2CoulLongSoft::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double denc,r,denlj,r4sig6,grij,expm2,t,erfc,prefactor;
|
||||
double fraction,forcecoul,forcelj,phicoul,philj;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
denc = sqrt(lj4[itype][jtype] + rsq);
|
||||
prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] /
|
||||
(denc*denc*denc);
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj));
|
||||
} else forcelj = 0.0;
|
||||
fforce = forcecoul + factor_lj*forcelj;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq) {
|
||||
prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
|
||||
phicoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
|
||||
eng += phicoul;
|
||||
}
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
philj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - offset[itype][jtype];
|
||||
eng += factor_lj*philj;
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJClass2CoulLongSoft::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 0;
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
||||
if (strcmp(str,"lambda") == 0) return (void *) lambda;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/class2/coul/long/soft,PairLJClass2CoulLongSoft)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CLASS2_COUL_LONG_SOFT_H
|
||||
#define LMP_PAIR_LJ_CLASS2_COUL_LONG_SOFT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJClass2CoulLongSoft : public Pair {
|
||||
public:
|
||||
PairLJClass2CoulLongSoft(class LAMMPS *);
|
||||
virtual ~PairLJClass2CoulLongSoft();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
virtual double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_lj_global;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double cut_coul,cut_coulsq;
|
||||
double **epsilon,**sigma, **lambda;
|
||||
double nlambda, alphalj, alphac;
|
||||
double **lj1,**lj2,**lj3,**lj4,**offset;
|
||||
double g_ewald;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style lj/class2/coul/long/soft requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
E: Pair style requires a KSpace style
|
||||
|
||||
No kspace style is defined.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,438 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cmath>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "pair_lj_class2_soft.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJClass2Soft::PairLJClass2Soft(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
allocated = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJClass2Soft::~PairLJClass2Soft()
|
||||
{
|
||||
if (!copymode) {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lambda);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(offset);
|
||||
allocated=0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,forcelj,factor_lj;
|
||||
double denlj, r4sig6;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2));
|
||||
fpair = factor_lj*forcelj;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
|
||||
evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lambda,n+1,n+1,"pair:lambda");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
nlambda = force->numeric(FLERR,arg[0]);
|
||||
alphalj = force->numeric(FLERR,arg[1]);
|
||||
|
||||
cut_global = force->numeric(FLERR,arg[2]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double epsilon_one = force->numeric(FLERR,arg[2]);
|
||||
double sigma_one = force->numeric(FLERR,arg[3]);
|
||||
double lambda_one = force->numeric(FLERR,arg[4]);
|
||||
if (sigma_one <= 0.0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
lambda[i][j] = lambda_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2Soft::init_one(int i, int j)
|
||||
{
|
||||
// always mix epsilon,sigma via sixthpower rules
|
||||
// mix distance via user-defined rule
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
|
||||
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
|
||||
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
|
||||
sigma[i][j] =
|
||||
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
|
||||
if (lambda[i][i] != lambda[j][j])
|
||||
error->all(FLERR,"Pair lj/class2/coul/cut/soft different lambda values in mix");
|
||||
lambda[i][j] = lambda[i][i];
|
||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||
}
|
||||
|
||||
lj1[i][j] = pow(lambda[i][j], nlambda);
|
||||
lj2[i][j] = pow(sigma[i][j], 6.0);
|
||||
lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
|
||||
|
||||
if (offset_flag && (cut[i][j] > 0.0)) {
|
||||
double denlj = lj3[i][j] + pow(cut[i][j] / sigma[i][j], 6.0);
|
||||
offset[i][j] = lj1[i][j] * epsilon[i][j] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj);
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
epsilon[j][i] = epsilon[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
lambda[j][i] = lambda[i][j];
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// compute I,J contribution to long-range tail correction
|
||||
// count total # of atoms of type I and J via Allreduce
|
||||
|
||||
if (tail_flag) {
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double count[2],all[2];
|
||||
count[0] = count[1] = 0.0;
|
||||
for (int k = 0; k < nlocal; k++) {
|
||||
if (type[k] == i) count[0] += 1.0;
|
||||
if (type[k] == j) count[1] += 1.0;
|
||||
}
|
||||
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
|
||||
double sig6 = sig3*sig3;
|
||||
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
|
||||
double rc6 = rc3*rc3;
|
||||
// check the following expressions for etail_lj & ptail_ij they are not correct !
|
||||
etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
|
||||
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
|
||||
ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
|
||||
sig6 * (sig3 - 2.0*rc3) / rc6;
|
||||
}
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||
fwrite(&lambda[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
fread(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||
fread(&lambda[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&nlambda,sizeof(double),1,fp);
|
||||
fwrite(&alphalj,sizeof(double),1,fp);
|
||||
fwrite(&cut_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
fwrite(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&nlambda,sizeof(double),1,fp);
|
||||
fread(&alphalj,sizeof(double),1,fp);
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
fread(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2Soft::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
|
||||
lambda[i][j],cut[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2Soft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
|
||||
double /*factor_coul*/, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double forcelj,philj;
|
||||
double r4sig6, denlj;
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj));
|
||||
} else forcelj = 0.0;
|
||||
fforce = factor_lj*forcelj;
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
denlj = lj3[itype][jtype] + rsq*rsq*rsq / lj2[itype][jtype];
|
||||
philj = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
|
||||
offset[itype][jtype];
|
||||
} else philj = 0.0;
|
||||
|
||||
return factor_lj*philj;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJClass2Soft::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
||||
if (strcmp(str,"lambda") == 0) return (void *) lambda;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/class2/soft,PairLJClass2Soft)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CLASS2_SOFT_H
|
||||
#define LMP_PAIR_LJ_CLASS2_SOFT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJClass2Soft : public Pair {
|
||||
public:
|
||||
PairLJClass2Soft(class LAMMPS *);
|
||||
virtual ~PairLJClass2Soft();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **epsilon, **sigma, **lambda;
|
||||
double nlambda, alphalj;
|
||||
double **lj1,**lj2,**lj3,**offset;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
E: Illegal ... command
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair lj/cut/soft different lambda values in mix
|
||||
The value of lambda has to be the same for I J pairs.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue