Reset some files back to upstream.

# 3d Lennard-Jones melt

units		lj

atom_style	atomic

lattice		fcc 0.8442

region		box block 0 10 0 10 0 10

create_box	1 box

create_atoms	1 box

mass		1 1.0

velocity	all create 3.0 87287

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no

fix		1 all nve

#dump		id all atom 50 dump.melt

#dump		2 all image 25 image.*.jpg type type &

#		axes yes 0.8 0.02 view 60 -30

#dump_modify	2 pad 3

#dump		3 all movie 25 movie.mpg type type &

#		axes yes 0.8 0.02 view 60 -30

#dump_modify	3 pad 3

thermo		50

run		250

# Solvated 5-mer peptide

units		real

atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0

bond_style      harmonic

angle_style     charmm

dihedral_style  charmm

improper_style  harmonic

kspace_style	pppm 0.0001

read_data	data.peptide

neighbor	2.0 bin

neigh_modify	delay 5

timestep	2.0

thermo_style	multi

thermo		50

fix		1 all nvt temp 275.0 275.0 100.0 tchain 1

fix		2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31

group		peptide type <= 12

#dump		1 peptide atom 10 dump.peptide

#dump		2 peptide image 25 image.*.jpg type type &

#		axes yes 0.8 0.02 view 60 -30 bond atom 0.5

#dump_modify	2 pad 3

#dump		3 peptide movie 25 movie.mpg type type &

#		axes yes 0.8 0.02 view 60 -30 bond atom 0.5

#dump_modify	3 pad 3

#compute		bnd all property/local btype batom1 batom2

#dump		2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]

run		300

# Simple rigid body system

units		lj

atom_style	atomic

pair_style	lj/cut 2.5

read_data	data.rigid

velocity 	all create 100.0 4928459

# unconnected bodies

group		clump1 id <> 1 9

group		clump2 id <> 10 18

group		clump3 id <> 19 27

group		clump4 id <> 28 36

group		clump5 id <> 37 45

group		clump6 id <> 46 54

group		clump7 id <> 55 63

group		clump8 id <> 64 72

group		clump9 id <> 73 81

fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &

	  	      clump6 clump7 clump8 clump9

# 1 chain of connected bodies

#group		clump1 id <> 1 9

#group		clump2 id <> 9 18

#group		clump3 id <> 18 27

#group		clump4 id <> 27 36

#group		clump5 id <> 36 45

#group		clump6 id <> 45 54

#group		clump7 id <> 54 63

#group		clump8 id <> 63 72

#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &

#	  	      clump6 clump7 clump8 clump9

# 2 chains of connected bodies

#group		clump1 id <> 1 9

#group		clump2 id <> 9 18

#group		clump3 id <> 18 27

#group		clump4 id <> 27 36

#group		clump5 id <> 37 45

#group		clump6 id <> 45 54

#group		clump7 id <> 54 63

#group		clump8 id <> 63 72

#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4

#fix 2 all poems group clump5 clump6 clump7 clump8 clump9

neigh_modify	exclude group clump1 clump1

neigh_modify	exclude group clump2 clump2

neigh_modify	exclude group clump3 clump3

neigh_modify	exclude group clump4 clump4

neigh_modify	exclude group clump5 clump5

neigh_modify	exclude group clump6 clump6

neigh_modify	exclude group clump7 clump7

neigh_modify	exclude group clump8 clump8

neigh_modify	exclude group clump9 clump9

thermo		100

#dump		1 all atom 50 dump.rigid

#dump		2 all image 100 image.*.jpg type type &

#		axes yes 0.8 0.02 view 60 -30

#dump_modify	2 pad 5

#dump		3 all movie 100 movie.mpg type type &

#		axes yes 0.8 0.02 view 60 -30

#dump_modify	3 pad 5

timestep 	0.0001

thermo		50

run		10000

# /* ----------------------------------------------------------------------   

#  Generic Linux Makefile for CUDA 

#     - Change CUDA_ARCH for your GPU

# ------------------------------------------------------------------------- */

# which file will be copied to Makefile.lammps

EXTRAMAKE = Makefile.lammps.standard

ifeq ($(CUDA_HOME),)

CUDA_HOME = /usr/local/cuda

endif

NVCC = nvcc

# Tesla CUDA

CUDA_ARCH = -arch=sm_21

# newer CUDA

#CUDA_ARCH = -arch=sm_13

# older CUDA

#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE

CUDA_ARCH = -arch=sm_35

# this setting should match LAMMPS Makefile

# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL

LMP_INC = -DLAMMPS_SMALLBIG

# precision for GPU calculations

# -D_SINGLE_SINGLE  # Single precision for all calculations

# -D_DOUBLE_DOUBLE  # Double precision for all calculations

# -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double

CUDA_PRECISION = -D_SINGLE_DOUBLE

CUDA_INCLUDE = -I$(CUDA_HOME)/include

CUDA_LIB = -L$(CUDA_HOME)/lib64

CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC

CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC

CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias

BIN_DIR = ./

OBJ_DIR = ./

LIB_DIR = ./

AR = ar

BSH = /bin/sh

CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini

include Nvidia.makefile

CXXFLAGS=$(CCFLAGS)

# Options: Cuda,ROCm,OpenMP,Pthreads,Qthreads,Serial

KOKKOS_DEVICES ?= "Cuda, OpenMP"

KOKKOS_DEVICES ?= "OpenMP"

#KOKKOS_DEVICES ?= "Pthreads"

# Options: 

KOKKOS_ARCH ?= "Pascal61"

# Intel:    KNC,KNL,SNB,HSW,BDW,SKX

# NVIDIA:   Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61

# ARM:      ARMv80,ARMv81,ARMv8-ThunderX

# IBM:      BGQ,Power7,Power8,Power9

# AMD-GPUS: Kaveri,Carrizo,Fiji,Vega

# AMD-CPUS: AMDAVX,Ryzen,Epyc

KOKKOS_ARCH ?= ""

# Options: yes,no

KOKKOS_DEBUG ?= "no"

# Options: hwloc,librt,experimental_memkind