Undid incorrect deletion of files.

variable number	equal 2

variable ofreq	equal 1000

variable efreq	equal 1000

variable T      equal 0.1

units lj

dimension 3

newton off

boundary  p p p

atom_style hybrid bond ellipsoid

atom_modify sort 0 1.0

# Pair interactions require lists of neighbours to be calculated

neighbor 1.0 bin

neigh_modify every 1 delay 0 check yes

read_data data.duplex2

set atom * mass 3.1575

group all type 1 4

# oxDNA bond interactions - FENE backbone

bond_style oxdna2/fene

bond_coeff * 2.0 0.25 0.7564

# oxDNA pair interactions

pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh

pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32

pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 

pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793

pair_coeff * * oxdna2/dh      ${T} 1.0 0.815

# NVE ensemble

#fix 1 all nve/dot

fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10

#fix 1 all nve/asphere

#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10

timestep 1e-5

#comm_style tiled

#fix 3 all balance 10000 1.1 rcb

#compute mol all chunk/atom molecule

#compute mychunk all vcm/chunk mol

#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector

#dump pos all xyz ${ofreq} traj.${number}.xyz

#compute quat all property/atom quatw quati quatj quatk

#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]

#dump_modify quat sort id

#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"

compute erot all erotate/asphere

compute ekin all ke

compute epot all pe

variable erot equal c_erot

variable ekin equal c_ekin

variable epot equal c_epot

variable etot equal c_erot+c_ekin+c_epot

fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes

#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz

#dump_modify out sort id

#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"

run 1000000

#write_restart config.${number}.*

# kokkos_cuda_mpi = KOKKOS/CUDA package, MPICH or OpenMPI with nvcc compiler, Kepler GPU

SHELL = /bin/sh

# ---------------------------------------------------------------------

# compiler/linker settings

# specify flags and libraries needed for your compiler

KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)

export MPICH_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper

export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper

CC =		mpicxx

CCFLAGS =	-g -O3

SHFLAGS =	-fPIC

DEPFLAGS =	-M

LINK =		mpicxx

LINKFLAGS =	-g -O3

LIB = 

SIZE =		size

ARCHIVE =	ar

ARFLAGS =	-rc

SHLIBFLAGS =	-shared

KOKKOS_DEVICES = Cuda

KOKKOS_ARCH = Kepler35

# ---------------------------------------------------------------------

# LAMMPS-specific settings, all OPTIONAL

# specify settings for LAMMPS features you will use

# if you change any -D setting, do full re-compile after "make clean"

# LAMMPS ifdef settings

# see possible settings in Section 2.2 (step 4) of manual

LMP_INC =	-DLAMMPS_GZIP

# MPI library

# see discussion in Section 2.2 (step 5) of manual

# MPI wrapper compiler/linker can provide this info

# can point to dummy MPI library in src/STUBS as in Makefile.serial

# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts

# INC = path for mpi.h, MPI compiler settings

# PATH = path for MPI library

# LIB = name of MPI library

MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1

MPI_PATH = 

MPI_LIB =	

# FFT library

# see discussion in Section 2.2 (step 6) of manaul

# can be left blank to use provided KISS FFT library

# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings

# PATH = path for FFT library

# LIB = name of FFT library

FFT_INC =    	

FFT_PATH = 

FFT_LIB =	

# JPEG and/or PNG library

# see discussion in Section 2.2 (step 7) of manual

# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC

# INC = path(s) for jpeglib.h and/or png.h

# PATH = path(s) for JPEG library and/or PNG library

# LIB = name(s) of JPEG library and/or PNG library

JPG_INC =       

JPG_PATH = 	

JPG_LIB =	

# ---------------------------------------------------------------------

# build rules and dependencies

# do not edit this section

include	Makefile.package.settings

include	Makefile.package

EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)

EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)

EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)

EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)

EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

# Path to src files

vpath %.cpp ..

vpath %.h ..

# Link target

$(EXE):	$(OBJ) $(EXTRA_LINK_DEPENDS)

	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)

	$(SIZE) $(EXE)

# Library targets

lib:	$(OBJ) $(EXTRA_LINK_DEPENDS)

	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)

shlib:	$(OBJ) $(EXTRA_LINK_DEPENDS)

	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \

        $(OBJ) $(EXTRA_LIB) $(LIB)

# Compilation rules

%.o:%.cpp $(EXTRA_CPP_DEPENDS)

	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

%.d:%.cpp $(EXTRA_CPP_DEPENDS)

	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@

%.o:%.cu $(EXTRA_CPP_DEPENDS)

	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

# Individual dependencies

depend : fastdep.exe $(SRC)

	@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1

fastdep.exe: ../DEPEND/fastdep.c

	cc -O -o $@ $<

sinclude .depend