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min latte partially fixed

This commit is contained in:
Christian Negre 2017-02-23 18:20:02 -07:00
parent 6d47cf350c
commit 2dcbc805ba
8 changed files with 240 additions and 4 deletions
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63
examples/latte/data.sucrose_non_opt.lmp Normal file
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@ -0,0 +1,63 @@
LAMMPS Description
45 atoms
3 atom types
0.0000000000000000 18.917000000000002 xlo xhi
0.0000000000000000 17.350999999999999 ylo yhi
0.0000000000000000 15.472000000000000 zlo zhi
Masses
1 15.994915008544922
2 12.000000000000000
3 1.0078250169754028
Atoms
1 1 1 0.0 11.47359 7.39174 7.26456
2 1 2 0.0 12.66159 8.24474 7.53356
3 1 3 0.0 13.49759 7.72474 7.00656
4 1 2 0.0 12.92859 8.18374 9.02956
5 1 1 0.0 13.69659 9.10274 10.46556
6 1 2 0.0 12.83959 10.10474 6.64056
7 1 3 0.0 13.24359 10.33074 7.58456
8 1 1 0.0 13.17359 9.67874 5.60956
9 1 2 0.0 11.20559 10.26374 6.86456
10 1 3 0.0 11.22159 11.15674 6.18156
11 1 1 0.0 10.78559 10.69674 8.19156
12 1 2 0.0 10.23459 9.20474 6.34356
13 1 3 0.0 9.23359 9.62574 6.11656
14 1 1 0.0 10.73959 8.65074 5.08856
15 1 2 0.0 10.18759 8.08774 7.38056
16 1 3 0.0 10.03259 8.49174 8.42656
17 1 1 0.0 9.22959 7.03374 7.08156
18 1 2 0.0 7.79359 7.27874 7.34356
19 1 1 0.0 7.44259 8.64274 6.96956
20 1 2 0.0 7.01059 9.43674 8.13856
21 1 3 0.0 5.95059 9.74974 7.96256
22 1 2 0.0 7.08359 8.51474 9.35656
23 1 3 0.0 8.19359 8.08474 9.80956
24 1 1 0.0 5.86059 8.56174 10.14056
25 1 2 0.0 7.34259 7.10674 8.80356
26 1 3 0.0 6.37259 6.54074 8.80556
27 1 1 0.0 8.32159 6.38474 9.58156
28 1 2 0.0 7.89859 10.67174 8.17156
29 1 1 0.0 6.06859 12.11474 7.59256
30 1 2 0.0 7.47359 7.05174 5.99256
31 1 1 0.0 5.66359 6.54374 6.50656
32 1 3 0.0 12.00659 8.11374 9.61556
33 1 3 0.0 13.35859 7.21774 9.30856
34 1 3 0.0 13.67759 8.46774 11.22956
35 1 3 0.0 12.44459 9.34474 5.00556
36 1 3 0.0 11.54859 11.18274 8.59756
37 1 3 0.0 11.00959 7.71574 5.30056
38 1 3 0.0 5.09459 8.45474 9.52056
39 1 3 0.0 7.92859 6.23074 10.47756
40 1 3 0.0 8.53259 10.62974 7.23156
41 1 3 0.0 8.58159 10.63874 9.05856
42 1 3 0.0 6.42359 13.37374 7.86056
43 1 3 0.0 7.58559 6.90074 4.62256
44 1 3 0.0 7.35159 5.27974 6.61456
45 1 3 0.0 5.22759 6.18974 5.69256

41
examples/latte/data.water Normal file
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@ -0,0 +1,41 @@
LAMMPS Description
24 atoms
2 atom types
0.0000000000000000 6.2670000000000003 xlo xhi
0.0000000000000000 6.2670000000000003 ylo yhi
0.0000000000000000 6.2670000000000003 zlo zhi
Masses
1 15.994915008544922
2 1.0078250169754028
Atoms
1 1 1 0.0 3.08800 3.70000 3.12400
2 1 2 0.0 4.05800 3.70000 3.12400
3 1 2 0.0 2.76400 3.13200 3.84100
4 1 1 0.0 2.47000 0.39000 1.36000
5 1 2 0.0 1.54000 0.37000 1.73000
6 1 2 0.0 2.48000 0.00000 0.44000
7 1 1 0.0 1.99300 0.41700 5.25000
8 1 2 0.0 2.39300 1.32700 5.16000
9 1 2 0.0 0.99300 0.49700 5.31000
10 1 1 0.0 2.05300 6.09700 3.48000
11 1 2 0.0 2.12300 5.20700 3.02000
12 1 2 0.0 1.11300 0.17000 3.40000
13 1 1 0.0 4.90000 5.37700 2.14000
14 1 2 0.0 5.51000 6.17700 2.18000
15 1 2 0.0 3.95000 5.68700 2.21000
16 1 1 0.0 0.92000 3.82700 0.56000
17 1 2 0.0 0.00000 3.54700 0.27000
18 1 2 0.0 1.23000 4.59700 0.00000
19 1 1 0.0 0.89000 2.03700 3.41000
20 1 2 0.0 0.72000 2.86700 2.87000
21 1 2 0.0 1.79000 1.66700 3.19000
22 1 1 0.0 4.45000 4.61700 5.43000
23 1 2 0.0 4.75000 3.89700 4.81000
24 1 2 0.0 4.06000 4.21700 6.26000

42
examples/latte/in.latte.sucrose.min Normal file
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@ -0,0 +1,42 @@
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
#read_data data.water
read_data data.sucrose_non_opt.lmp
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal
# minimization
thermo 1
min_style cg
minimize 1.0e-9 1.0e-9 1000 1000

40
examples/latte/in.latte.water Normal file
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@ -0,0 +1,40 @@
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal
# dynamics
thermo 10
run 100

41
examples/latte/in.latte.water.min Normal file
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@ -0,0 +1,41 @@
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal
# minimization
thermo 1
min_style fire
minimize 1.0e-9 1.0e-9 1000 1000

4
lib/latte/README
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@ -20,7 +20,7 @@ follow these steps:
- Set the MAKELIB flag to ON in makefile.CHOICES and finally, build the
code with the make command.
Note that if you unpack and build LATTE in this directory, if you
Note that if you unpack and build LATTE in this directory and you
download a new LAMMPS tarball, the files you have added here will be
lost. So you likely want to build it somewhere else. The recommended
place is the home directory.
@ -28,7 +28,7 @@ place is the home directory.
To build LAMMPS with the LATTE library you should follow the following
instructions:
- makefile.lammps.* to makefile.lammps in the /lammps/lib/latte directory.
- copy makefile.lammps.* to makefile.lammps in the /lammps/lib/latte directory.
- Change the path, flags and compilers on the makefile.lammps according
to your compilers, architecture and the LATTE location.

12
src/LATTE/fix_latte.cpp
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@ -45,7 +45,8 @@ using namespace FixConst;
extern "C" {
void latte(int *, int *, double *, int *, int *,
double *, double *, double *, double *, int*, double *, double *, double *);
double *, double *, double *, double *, int*,
double *, double *, double *);
}
#define INVOKED_PERATOM 8
@ -282,7 +283,7 @@ void FixLatte::post_force(int vflag)
int maxiter = -1;
latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,
forces,&maxiter, &latte_energy, &atom->v[0][0],&update->dt);
forces,&maxiter,&latte_energy,&atom->v[0][0],&update->dt);
// sum LATTE forces to LAMMPS (Coulombic) forces
@ -297,6 +298,13 @@ void FixLatte::post_force(int vflag)
}
}
/* ---------------------------------------------------------------------- */
void FixLatte::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
integrate electronic degrees of freedom
------------------------------------------------------------------------- */

1
src/LATTE/fix_latte.h
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@ -36,6 +36,7 @@ class FixLatte : public Fix {
void initial_integrate(int);
void pre_reverse(int, int);
void post_force(int);
void min_post_force(int);
void final_integrate();
void reset_dt();
double compute_scalar();