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Automatically exported from code.google.com/p/lammps-induced-dipole-polarization-pair-style

License: GNU General Public License v2.0

Tcl 10.03% C 1.44% C++ 74.31% Fortran 4.13% Makefile 0.27% Gnuplot 0.01% Cuda 1.67% Shell 0.86% Python 4.55% Roff 0.28% CMake 0.37% xBase 0.01% Perl 0.33% Jupyter Notebook 1.10% Emacs Lisp 0.01% Vim Script 0.01% Arc 0.14% MATLAB 0.06% TeX 0.45% Awk 0.01%

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lammps-induced-dipole-polarization-pair-style's Issues

compiler and run errors

Hi,

I met errors when compile:

$ make mpi
make[1]: Entering directory `/HOME/nscc-gz_pinchen/sf_box/lammps-PIM2/lammps-induced-dipole-polarization-pair-style/src/Obj_mpi'
cc -O -o fastdep.exe ../DEPEND/fastdep.c
make[1]: Leaving directory `/HOME/nscc-gz_pinchen/sf_box/lammps-PIM2/lammps-induced-dipole-polarization-pair-style/src/Obj_mpi'
make[1]: Entering directory `/HOME/nscc-gz_pinchen/sf_box/lammps-PIM2/lammps-induced-dipole-polarization-pair-style/src/Obj_mpi'
mpicxx -g -O3   -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64  -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/local/mpi3-dynamic/include -I/WORK/app/intel/composer_xe_2015.1.133/mkl/include/fftw   -c ../angle.cpp
mpicxx -g -O3   -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64  -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/local/mpi3-dynamic/include -I/WORK/app/intel/composer_xe_2015.1.133/mkl/include/fftw   -c ../angle_hybrid.cpp
mpicxx -g -O3   -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64  -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/local/mpi3-dynamic/include -I/WORK/app/intel/composer_xe_2015.1.133/mkl/include/fftw   -c ../angle_zero.cpp
mpicxx -g -O3   -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64  -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/local/mpi3-dynamic/include -I/WORK/app/intel/composer_xe_2015.1.133/mkl/include/fftw   -c ../atom.cpp
../atom.cpp(23): catastrophic error: cannot open source file "atom_vec_ellipsoid.h"
  #include "atom_vec_ellipsoid.h"
                                 ^

compilation aborted for ../atom.cpp (code 4)
make[1]: *** [atom.o] Error 4
make[1]: Leaving directory `/HOME/nscc-gz_pinchen/sf_box/lammps-PIM2/lammps-induced-dipole-polarization-pair-style/src/Obj_mpi'
make: *** [mpi] Error 2

Then I copy atom_vec_ellipsoid.h from src of lammps-31Mar17; then some miss files like:accelerator_kokkos.h, dihedral_hybrid*,improper_hybrid.*,math_complex.h...

and then:

mpicxx -g -O3   -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64  -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/local/mpi3-dynamic/include -I/WORK/app/intel/composer_xe_2015.1.133/mkl/include/fftw   -c ../special.cpp
../special.cpp(595): error: pointer to incomplete class type is not allowed
      memoryKK->grow_kokkos(atomKK->k_special,atom->special,
      ^

compilation aborted for ../special.cpp (code 2)
make[1]: *** [special.o] Error 2

I do not need kokkos, so i comment out this line in special.cpp. Finally, The compilation passed. When I test Bulk H2 example, I got an error:

Reading data file ...
  orthogonal box = (-10.7974 -10.7974 -10.7974) to (10.7974 10.7974 10.7974)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  750 atoms
  scanning bonds ...
  4 = max bonds/atom
  reading bonds ...
  600 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:   0          0          0         
  special bond factors coul: 0          0          0         
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors
Setting atom values ...
ERROR: Cannot set this attribute for this atom style (../set.cpp:179)
Last command: set type 1 static_polarizability 0.69380 #H2G
yhrun: error: cn10986: task 0: Exited with exit code 1

I found that the static_polarizability_flag could not get vaule, So I give 1 to static_polarizability_flag directly in atom.cpp, but error still occured：

yhrun -n 1 lmp_mpi -in h2.input
.....
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:   0          0          0         
  special bond factors coul: 0          0          0         
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors
Setting atom values ...
yhrun: error: cn10432: task 0: Segmentation fault

I tracked this bug for missing creating memory for static_polarizability. Then I met a lot of errors of "Segmentation fault".

Finally, I want to ask if I make a mistake when compile, or my compiling environment is wrong? I found that you have executed the example of Bulk H2 with log.lammps, or the current version of lammps is not stable?

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