Skip to content

Instantly share code, notes, and snippets.

View derekbrokeit's full-sized avatar

Derek Ashley Thomas derekbrokeit

8 followers · 0 following
  • Moffett Field, CA
View GitHub Profile
@derekbrokeit
derekbrokeit / smooth_airebo.diff
Created November 20, 2013 05:46
smooth cutoff function for LAMMPS airebo
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index f655506..b424e91 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -713,9 +713,12 @@ void PairAIREBO::FLJ(int eflag, int vflag)
sigcut = 3.0;
sigmin = sigcut - sigwid;
- rljmin = sigma[itype][jtype];
- rljmax = sigcut * rljmin;
@derekbrokeit
derekbrokeit / gist:6789587
Created October 2, 2013 05:44
Complete compilation and installation of numpy 1.8rc1 using command: `python3 setup.py build --compiler=intelem --fcompiler=intelem install --prefix=$HOME/no-xhost` compiler setup as follows: intelccompiler.py: `self.cc_exe = 'icc -m64 -fPIC -O0'` fcompiler/intel.py: `return ['-xhost -openmp -O0']` Results in errors given [here](https://gist.git…
F2PY Version 2
blas_opt_info:
blas_mkl_info:
FOUND:
include_dirs = ['/opt/intel/composerxe-2011.1.107/mkl/include']
library_dirs = ['/home/derekt/.linuxbrew/lib']
libraries = ['mkl_custom', 'pthread']
define_macros = [('SCIPY_MKL_H', None)]
FOUND:
@derekbrokeit
derekbrokeit / numpy1.8r1_test_fail.log
Created October 1, 2013 02:02
compiled with icc/ifort and mkl in python 3.3.2
Running unit tests for numpy
NumPy version 1.8.0rc1
NumPy is installed in /home/derekt/.linuxbrew/lib/python3.3/site-packages/numpy
Python version 3.3.2 (default, Oct 1 2013, 09:31:14) [GCC Intel(R) C++ gcc 4.1 mode]
nose version 1.3.0
..................S..........S.........................................................................................................................................................S......................................................................
..............................................................................................................................................................................................................................................................
..............................................................................................................................................................................................................................................................
......................
@derekbrokeit
derekbrokeit / lammps-fix-time.diff
Last active December 20, 2015 08:09
Fix a temporary bug in lammps with a undefined function call
diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/USER-OMP/pair_tip4p_cut_omp.cpp
index 536d633..8f288a6 100644
--- a/src/USER-OMP/pair_tip4p_cut_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_cut_omp.cpp
@@ -101,7 +101,7 @@ void PairTIP4PCutOMP::compute(int eflag, int vflag)
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
- thr->timer(ThrData::TIME_START);
+ /* thr->timer(ThrData::TIME_START); */
@derekbrokeit
derekbrokeit / h5py_failed_tests.log
Created July 17, 2013 00:07
h5py failure on opensuse. hdf5 (1.8.11) and python (2.7.4) built by linuxbrew Same as: https://github.com/h5py/h5py/issues/304
...........................................sss...............................................E.....EFF..F....F.Es.......................................................................................x.............................................
======================================================================
ERROR: test_create_scale (h5py._hl.tests.test_dimension_scales.TestDimensionManager)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/derekt/.linuxbrew/lib/python2.7/site-packages/h5py/_hl/tests/test_dimension_scales.py", line 101, in test_create_scale
self.assertEqual(self.f['data'].dims[2]['foobar'], self.f['x1'])
File "/home/derekt/.linuxbrew/lib/python2.7/site-packages/h5py/_hl/dims.py", line 54, in __getitem__
raise KeyError('%s not found' % item)
KeyError: 'foobar not found'
@derekbrokeit
derekbrokeit / lammps_airebo_test.diff
Created June 13, 2013 04:10
Testing extent to which airebo can be modified for better graphite
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 6e1edb1..1d491d0 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -709,6 +709,9 @@ void PairAIREBO::FLJ(int eflag, int vflag)
rljmax = sigcut * rljmin;
rljmin = sigmin * rljmin;
+ rljmin = 3.816370964251868;
+ rljmax = cutlj * sigma[itype][jtype];
@derekbrokeit
derekbrokeit / torch7_serial.rb
Created May 24, 2013 08:14
A homebrew formula copy of torch7 that builds without OpenMP support. Additionally, it builds with significantly reduced dependencies.
require 'formula'
class Torch7 < Formula
homepage 'http://www.torch.ch/'
head 'https://github.com/andresy/torch.git'
url 'https://github.com/andresy/torch/archive/7.0.3-0.zip'
version '7.0.3-0'
sha1 'd455003b3f632ffd5062f98de774479c1de57607'
depends_on 'cmake' => :build
@derekbrokeit
derekbrokeit / python_disable_x11_lib.diff
Created April 16, 2013 08:09
Disable automatically linking to x11 in python installation.
diff --git a/setup.py b/setup.py
index ea8a5f5..5460fb9 100644
--- a/setup.py
+++ b/setup.py
@@ -1897,8 +1897,8 @@ class PyBuildExt(build_ext):
libs.append('ld')
# Finally, link with the X11 libraries (not appropriate on cygwin)
- if host_platform != "cygwin":
- libs.append('X11')
@derekbrokeit
derekbrokeit / povray_install_failure
Created February 25, 2013 05:50
Homebrew povray installation failure
==> Downloading http://www.povray.org/beta/source/povray-3.7.0.RC6.tar.gz
Already downloaded: /Library/Caches/Homebrew/povray-3.7.0.RC6.tar.gz
/usr/bin/tar xf /Library/Caches/Homebrew/povray-3.7.0.RC6.tar.gz
==> Downloading patches
/usr/bin/curl -f#LA Homebrew 0.9.4 (Ruby 1.8.7-358; Mac OS X 10.8.2) https://trac.macports.org/export/102440/trunk/dports/graphics/povray/files/patch-boost-1.50.diff -o 000-homebrew.diff https://trac.macports.org/export/102440/trunk/dports/graphics/povray/files/patch-configure-stat.diff -o 001-homebrew.diff https://trac.macports.org/export/102440/trunk/dports/graphics/povray/files/patch-lseek64.diff -o 002-homebrew.diff https://trac.macports.org/export/102440/trunk/dports/graphics/povray/files/patch-vfe-uint.diff -o 003-homebrew.diff --silent
==> Patching
/usr/bin/patch -f -p0 -i 000-homebrew.diff
patching file source/backend/scene/view.cpp
patching file source/base/timer.cpp
patching file vfe/unix/platformbase.cpp
@derekbrokeit
derekbrokeit / pymol_disable_vmd_plugin.diff
Created February 16, 2013 09:47
Disable VMD plugin in pymol
diff --git a/setup.py b/setup.py
index b8d7070..46d9087 100644
--- a/setup.py
+++ b/setup.py
@@ -118,7 +118,7 @@ lib_dirs = []
ext_comp_args = []
ext_link_args = []
-if True:
+if False: