[lammps-users] Typo on region doc page

Hi Steve-

Noticed a typo on the region doc page:

block args = dim c1 c2 radlo radhi lo hi
    xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
  cone args = xlo xhi ylo yhi zlo zhi
    dim = x or y or z = axis of cone...

The args for block and cone are switched. Might confuse someone new...

Erin

Hi experts,

I met this error when running the in.peptide in example folder, is this
about the FFTW library problem? Thanks!

Liang

The log file below,

LAMMPS (9 Jan 2009)
# 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
  3 = max bonds/atom
  6 = max angles/atom
  14 = max dihedrals/atom
  1 = max impropers/atom
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 1 by 2 processor grid
  2004 atoms
  2004 velocities
  1365 bonds
  786 angles
  207 dihedrals
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors

neighbor 2.0 bin
neigh_modify delay 5

timestep 0.1

thermo_style multi
thermo 10

fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
  19 = # of size 2 clusters
  6 = # of size 3 clusters
  3 = # of size 4 clusters
  640 = # of frozen angles

group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond

run 3000
PPPM initialization ...
  G vector = 0.268721
  grid = 15 15 15
  stencil order = 5
  RMS precision = 4.86052e-05
  brick FFT buffer size/proc = 6776 1800 5808
SHAKE stats (type/ave/delta) on step 0
  4 1.111 1.44264e-05
  6 0.996998 7.26967e-06
  8 1.08 1.32536e-05
  10 1.111 1.22749e-05
  12 1.08 1.11767e-05
  14 0.96 0
  18 0.957206 4.37979e-05
  31 104.519 0.00396029
Memory usage per processor = 10.0945 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec)

Hi experts,

I met this error when running the in.peptide in example folder, is this
about the FFTW library problem? Thanks!

no. it is about a miscompiled executable.
you are most likely using gcc-4.x as compiler and
need to add -fno-strict-aliasing to the command line
or adapt the Makefile.openmpi for your machine setup.

cheers,
   axel.

Fixed it - thanks

Steve

The doc page on building LAMMPS discusses this.

Steve