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tim |
1603 |
2004-10-18 23:34 tim |
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* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
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are fixed in Vector class |
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2004-10-18 23:28 tim |
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* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
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some bugs in RectMatrixTestCase |
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2004-10-18 23:21 tim |
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* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
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test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
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test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
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test/math/VectorTestCase.hpp: implement more test cases |
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2004-10-18 18:13 tim |
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* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
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src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
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src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
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src/utils/StringTokenizer.hpp, test/math/Makefile, |
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test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
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tests on math library |
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2004-10-18 16:03 tim |
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* test/math/: Makefile, QuaternionTestCase.cpp, |
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QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
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SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
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Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
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more testing units |
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2004-10-18 12:07 tim |
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* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
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math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
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math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
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utils/GenericFactory.hpp: fix some bugs in Quaternion class |
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2004-10-18 11:30 gezelter |
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* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
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Your basic run of the mill real-valued versions of Y_l^m(\theta, |
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\phi) |
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2004-10-18 11:29 gezelter |
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* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
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types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
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utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
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Shapes into OOPSE |
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2004-10-18 10:21 gezelter |
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* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
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2004-10-18 00:23 tim |
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* test/math/VectorTestCase.hpp: adding vector test case |
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2004-10-18 00:23 tim |
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* src/utils/GenericFactory.hpp: adding generic factory and vector |
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test case |
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tim |
1594 |
2004-10-16 20:19 tim |
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* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
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SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
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progress |
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2004-10-15 20:31 tim |
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* src/math/Quaternion.hpp: add quaternion class |
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2004-10-15 16:11 tim |
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* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
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IfstrstreamTestCase.hpp: adding test file |
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2004-10-15 16:10 tim |
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* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
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2004-10-15 15:42 tim |
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* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
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2004-10-15 15:35 tim |
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* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
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2004-10-15 15:34 tim |
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* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
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namespace oopse |
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2004-10-15 14:38 chuckv |
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* configure, ac-tools/aclocal.m4: Changed optimization flags for |
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XLF and XLC. |
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2004-10-15 13:28 tim |
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* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
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adding ifstrstream test case |
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2004-10-15 13:20 tim |
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* src/io/basic_ifstrstream.hpp: fix include |
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2004-10-15 13:18 tim |
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* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
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2004-10-15 13:17 tim |
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* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
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2004-10-15 13:16 tim |
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* test/io/: Makefile, ifstrstreamTestCase.cpp, |
| 125 |
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ifstrstreamTestCase.hpp: adding test case for ifstrstream |
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2004-10-15 10:37 tim |
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* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
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ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
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2004-10-15 10:20 tim |
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* src/io/basic_ifstrstream.hpp: add checkFilename Option |
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2004-10-15 10:19 tim |
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| 138 |
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* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
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SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
| 140 |
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SquareMatrixTestCase class |
| 141 |
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| 142 |
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2004-10-15 02:52 tim |
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| 144 |
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* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
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| 146 |
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2004-10-14 18:28 tim |
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| 148 |
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* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
| 149 |
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Vector.hpp: math library in progress |
| 150 |
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| 151 |
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2004-10-14 18:27 tim |
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* src/io/FileReader.hpp: FileReader in progress |
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2004-10-13 18:53 tim |
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* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
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test in isOrthogonal of SquareMatrix is failed by some reasons |
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| 160 |
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2004-10-13 17:28 tim |
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* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
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class |
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2004-10-13 17:27 tim |
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* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
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RectMatrixTestCase.hpp: adding testing unit |
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2004-10-13 17:24 tim |
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* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
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2004-10-13 01:51 tim |
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* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
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Vector3.hpp: refactory vector and matrix classes |
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2004-10-13 01:50 tim |
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* src/math/Vector3d.hpp: Remove some Makefile.in |
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2004-10-12 18:57 tim |
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* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
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Matrix3x3d.hpp |
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2004-10-12 14:08 tim |
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* doc/: cppstyle.html, style.css: adding c++ coding style |
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2004-10-11 17:15 tim |
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* src/: constraints/AbstractClasses.hpp, |
| 195 |
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integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
| 196 |
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change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
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2004-10-11 16:54 tim |
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* scripts/filepp: fix a bug in filepp |
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2004-10-11 16:13 tim |
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* make/Makefile.in: using filepp to generate dependencies instead |
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of compilers |
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2004-10-11 16:10 tim |
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* scripts/filepp: filepp can be used to generate dependencies for |
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c/c++ now |
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2004-10-11 13:40 tim |
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* make/Makefile.in: remove -module from F90Options |
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2004-10-11 13:01 tim |
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* make/Makefile.in: adding rules to move fortran 90 module to |
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target directory |
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2004-10-11 10:43 gezelter |
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* make/Makefile.in: fixed makefile.in |
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2004-10-11 09:51 tim |
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* scripts/filepp: remove "use bytes" which causes problem in sgi |
| 228 |
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machine |
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2004-10-11 09:26 tim |
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* forceFields/Makefile: add Makefile |
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2004-10-11 09:23 tim |
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* samples/: water/dimer/Makefile, water/spce/Makefile, |
| 237 |
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water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
| 238 |
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water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
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directory |
| 240 |
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| 241 |
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2004-10-11 09:23 tim |
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* samples/argon/Makefile: remove argon.dump and argon.eor from |
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Makefile |
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| 246 |
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2004-10-09 01:01 tim |
| 247 |
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* samples/: alkane/Makefile.in, argon/Makefile.in, |
| 249 |
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lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
| 250 |
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Remove some Makefile.in |
| 251 |
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| 252 |
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2004-10-08 18:15 tim |
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* make/Makefile.in: [no log message] |
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2004-10-08 17:51 tim |
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* make/Makefile.in: fix make install |
| 259 |
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2004-10-08 17:10 tim |
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* make/Makefile.in: adding make install |
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2004-10-08 17:04 tim |
| 265 |
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| 266 |
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* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 267 |
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metals/Makefile, minimizer/Makefile, water/Makefile.in, |
| 268 |
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water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
| 269 |
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water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
| 270 |
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water/ssde/Makefile, water/ssde/Makefile.in, |
| 271 |
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water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
| 272 |
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water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
| 273 |
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zcons/Makefile.in: add Makefile to sample directory |
| 274 |
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| 275 |
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2004-10-06 18:03 gezelter |
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| 277 |
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* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
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stuff |
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2004-10-06 18:03 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 283 |
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make/Doxyfile, src/applications/getopt.c, |
| 284 |
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src/applications/getopt1.c, src/applications/gnugetopt.h: more |
| 285 |
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build fixes |
| 286 |
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| 287 |
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2004-10-06 17:20 tim |
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| 289 |
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* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
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2004-10-06 17:19 tim |
| 292 |
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* scripts/filepp: filepp can handle different fortran module case |
| 294 |
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and suffix |
| 295 |
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| 296 |
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2004-10-06 16:27 gezelter |
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| 298 |
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* src/restraints/Restraints.cpp: Chris doesn't know about the |
| 299 |
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OOPSE-2.0 directory structure yet |
| 300 |
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2004-10-06 16:27 gezelter |
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* ChangeLog: Yeah yeah, we'lll get around to it later |
| 304 |
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| 305 |
gezelter |
1536 |
2004-10-06 16:22 gezelter |
| 306 |
gezelter |
1490 |
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| 307 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 308 |
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make/Makefile.in: cleaning up build process |
| 309 |
gezelter |
1490 |
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| 310 |
tim |
1594 |
2004-10-06 15:01 chrisfen |
| 311 |
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* src/restraints/Restraints.cpp: made the file reading in |
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restraints more intelligent - no longer gives uninformative seg |
| 314 |
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faults |
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2004-10-06 14:55 gezelter |
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* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
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| 320 |
gezelter |
1536 |
2004-10-06 14:51 gezelter |
| 321 |
gezelter |
1490 |
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tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
| 323 |
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scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
| 324 |
gezelter |
1490 |
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| 325 |
tim |
1594 |
2004-10-06 13:53 tim |
| 326 |
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* make/: Makefile, Makefile.in: fix make statistics |
| 328 |
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2004-10-06 13:18 tim |
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* make/: Makefile, Makefile.in: adding GNU make functions to |
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combine all of the static libraries to a big library |
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2004-10-05 17:57 tim |
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* make/: Makefile, Makefile.in: adding shared library flag |
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2004-10-05 14:37 tim |
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* src/: Makefile, UseTheForce/Makefile, |
| 341 |
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UseTheForce/mpiSimulation_module.F90, |
| 342 |
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UseTheForce/DarkSide/Makefile, |
| 343 |
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UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
| 344 |
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mpiSimulation_module to DarkSide |
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2004-10-05 14:35 tim |
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* make/: Makefile, Makefile.in: building MPI version;using static |
| 349 |
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library instead of shared library |
| 350 |
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| 351 |
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2004-10-05 09:14 tim |
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* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
| 354 |
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to filepp |
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2004-10-04 15:56 tim |
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* make/: Makefile, Makefile.in: add make cvslog |
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2004-10-04 11:24 gezelter |
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* make/: Makefile, Makefile.in: more work on the parallel build |
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2004-10-04 11:06 gezelter |
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* make/: Makefile, Makefile.in: changes to backport declare flags |
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2004-10-04 10:27 gezelter |
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* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
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DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
| 372 |
|
|
shapes |
| 373 |
|
|
|
| 374 |
|
|
2004-10-01 23:40 tim |
| 375 |
|
|
|
| 376 |
|
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
| 377 |
|
|
|
| 378 |
|
|
2004-10-01 23:22 tim |
| 379 |
|
|
|
| 380 |
|
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
| 381 |
|
|
|
| 382 |
|
|
2004-10-01 16:59 tim |
| 383 |
|
|
|
| 384 |
|
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
| 385 |
|
|
|
| 386 |
gezelter |
1536 |
2004-10-01 16:22 gezelter |
| 387 |
gezelter |
1490 |
|
| 388 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
| 389 |
|
|
few minor build changes |
| 390 |
gezelter |
1490 |
|
| 391 |
tim |
1594 |
2004-10-01 16:11 tim |
| 392 |
|
|
|
| 393 |
|
|
* scripts/filepp: adding fortran90 make dependency tool |
| 394 |
|
|
|
| 395 |
|
|
2004-09-30 10:41 tim |
| 396 |
|
|
|
| 397 |
|
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
| 398 |
|
|
remove object files belong to current package. turn off silent |
| 399 |
|
|
mode |
| 400 |
|
|
|
| 401 |
|
|
2004-09-29 16:55 tim |
| 402 |
|
|
|
| 403 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
| 404 |
|
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
| 405 |
|
|
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
| 406 |
|
|
brains/Makedepend, brains/Makefile, constraints/Makefile, |
| 407 |
|
|
integrators/Makefile, io/Makefile, math/Makefile, |
| 408 |
|
|
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
| 409 |
|
|
restraints/Makefile, types/Makefile, utils/Makefile, |
| 410 |
|
|
visitors/Makefile: define DEV_ROOT as relative path |
| 411 |
|
|
|
| 412 |
|
|
2004-09-29 16:54 tim |
| 413 |
|
|
|
| 414 |
|
|
* make/: Makefile, Makefile.in: get the relative path by shell |
| 415 |
|
|
script |
| 416 |
|
|
|
| 417 |
|
|
2004-09-29 16:32 tim |
| 418 |
|
|
|
| 419 |
|
|
* make/Makefile: eliminate DEV_ROOT by relative path |
| 420 |
|
|
|
| 421 |
|
|
2004-09-29 13:37 tim |
| 422 |
|
|
|
| 423 |
|
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
| 424 |
|
|
|
| 425 |
gezelter |
1536 |
2004-09-29 12:57 gezelter |
| 426 |
gezelter |
1490 |
|
| 427 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
| 428 |
gezelter |
1490 |
|
| 429 |
tim |
1594 |
2004-09-29 12:56 gezelter |
| 430 |
|
|
|
| 431 |
tim |
1603 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
| 432 |
tim |
1594 |
|
| 433 |
gezelter |
1536 |
2004-09-29 12:46 tim |
| 434 |
gezelter |
1490 |
|
| 435 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
| 436 |
gezelter |
1490 |
|
| 437 |
tim |
1594 |
2004-09-29 12:12 tim |
| 438 |
|
|
|
| 439 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
| 440 |
|
|
|
| 441 |
gezelter |
1536 |
2004-09-29 10:58 gezelter |
| 442 |
gezelter |
1490 |
|
| 443 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
| 444 |
gezelter |
1490 |
|
| 445 |
tim |
1594 |
2004-09-29 10:00 tim |
| 446 |
|
|
|
| 447 |
|
|
* make/Makefile: add print statment to rules |
| 448 |
|
|
|
| 449 |
|
|
2004-09-29 09:59 tim |
| 450 |
|
|
|
| 451 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
| 452 |
|
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
| 453 |
|
|
applications/simpleBuilder/Makefile, brains/Makefile, |
| 454 |
|
|
constraints/Makefile, integrators/Makefile, io/Makefile, |
| 455 |
|
|
math/Makefile, minimizers/Makefile, primitives/Makefile, |
| 456 |
|
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
| 457 |
|
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
| 458 |
|
|
|
| 459 |
|
|
2004-09-28 21:55 tim |
| 460 |
|
|
|
| 461 |
|
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
| 462 |
|
|
which cause headache in bulding libutils |
| 463 |
|
|
|
| 464 |
|
|
2004-09-28 18:24 tim |
| 465 |
|
|
|
| 466 |
|
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
| 467 |
|
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
| 468 |
|
|
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 469 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
| 470 |
|
|
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
| 471 |
|
|
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
| 472 |
|
|
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
| 473 |
|
|
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
| 474 |
|
|
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
| 475 |
|
|
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
| 476 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 477 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 478 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 479 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
| 480 |
|
|
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
| 481 |
|
|
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
| 482 |
|
|
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
| 483 |
|
|
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
| 484 |
|
|
change directory structure of application. Every executable file is |
| 485 |
|
|
replaced in seperate directory |
| 486 |
|
|
|
| 487 |
|
|
2004-09-28 17:15 gezelter |
| 488 |
|
|
|
| 489 |
|
|
* lib/dummy: Keep that lib around, please. |
| 490 |
|
|
|
| 491 |
gezelter |
1536 |
2004-09-28 17:14 gezelter |
| 492 |
gezelter |
1490 |
|
| 493 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
| 494 |
|
|
starting a configure version |
| 495 |
gezelter |
1490 |
|
| 496 |
tim |
1594 |
2004-09-28 16:08 tim |
| 497 |
|
|
|
| 498 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
| 499 |
|
|
UseTheForce/DarkSide/Makefile, |
| 500 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 501 |
|
|
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
| 502 |
|
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
| 503 |
|
|
around to solve dependency problem |
| 504 |
|
|
|
| 505 |
gezelter |
1536 |
2004-09-28 15:43 tim |
| 506 |
gezelter |
1490 |
|
| 507 |
tim |
1594 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
| 508 |
|
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
| 509 |
|
|
src/applications/Makedepend, src/applications/Makefile, |
| 510 |
|
|
src/brains/Makedepend, src/brains/simulation_module.F90, |
| 511 |
|
|
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
| 512 |
|
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
| 513 |
|
|
src/utils/Makefile: [no log message] |
| 514 |
gezelter |
1490 |
|
| 515 |
tim |
1594 |
2004-09-28 15:41 tim |
| 516 |
|
|
|
| 517 |
|
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
| 518 |
|
|
problem |
| 519 |
|
|
|
| 520 |
|
|
2004-09-28 11:13 tim |
| 521 |
|
|
|
| 522 |
|
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
| 523 |
|
|
src/io/Makefile: add yacc and lex rules |
| 524 |
|
|
|
| 525 |
|
|
2004-09-27 15:24 tim |
| 526 |
|
|
|
| 527 |
|
|
* make/Makefile: adding include path to F90Options |
| 528 |
|
|
|
| 529 |
|
|
2004-09-27 15:13 tim |
| 530 |
|
|
|
| 531 |
|
|
* make/Makefile: change suffix from .cc to .cpp |
| 532 |
|
|
|
| 533 |
|
|
2004-09-24 11:27 tim |
| 534 |
|
|
|
| 535 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 536 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 537 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
| 538 |
|
|
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
| 539 |
|
|
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
| 540 |
|
|
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
| 541 |
|
|
UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 542 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 543 |
|
|
UseTheForce/DarkSide/switch_module.F90, |
| 544 |
|
|
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
| 545 |
|
|
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
| 546 |
|
|
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
| 547 |
|
|
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
| 548 |
|
|
applications/MoLocator.cpp, applications/MoLocator.hpp, |
| 549 |
|
|
applications/cmdline.c, applications/nanoBuilder.cpp, |
| 550 |
|
|
applications/oopse.cpp, applications/simpleBuilder.cpp, |
| 551 |
|
|
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
| 552 |
|
|
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 553 |
|
|
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
| 554 |
|
|
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 555 |
|
|
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
| 556 |
|
|
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
| 557 |
|
|
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
| 558 |
|
|
integrators/Integrator.hpp, integrators/NPT.cpp, |
| 559 |
|
|
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
| 560 |
|
|
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
| 561 |
|
|
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
| 562 |
|
|
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
| 563 |
|
|
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
| 564 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 565 |
|
|
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
| 566 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
| 567 |
|
|
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
| 568 |
|
|
math/MatVec3.h, math/randomSPRNG.cpp, |
| 569 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
| 570 |
|
|
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
| 571 |
|
|
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
| 572 |
|
|
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
| 573 |
|
|
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
| 574 |
|
|
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
| 575 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 576 |
|
|
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
| 577 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 578 |
|
|
primitives/RigidBody.hpp, primitives/SRI.hpp, |
| 579 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 580 |
|
|
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
| 581 |
|
|
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
| 582 |
|
|
restraints/Restraints.hpp, types/AtomStamp.cpp, |
| 583 |
|
|
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
| 584 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
| 585 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 586 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 587 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 588 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 589 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 590 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
| 591 |
|
|
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
| 592 |
|
|
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
| 593 |
|
|
utils/simError.c, visitors/AtomVisitor.cpp, |
| 594 |
|
|
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 595 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 596 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 597 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 598 |
|
|
visitors/ZconsVisitor.hpp: change the #include in source files |
| 599 |
|
|
|
| 600 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
| 601 |
gezelter |
1490 |
|
| 602 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 603 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 604 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 605 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 606 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 607 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 608 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 609 |
|
|
src/UseTheForce/fForceField.h, |
| 610 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
| 611 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
| 612 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
| 613 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
| 614 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
| 615 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 616 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
| 617 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 618 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
| 619 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 620 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 621 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 622 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
| 623 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
| 624 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 625 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 626 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
| 627 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
| 628 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 629 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
| 630 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 631 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 632 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 633 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 634 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 635 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 636 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 637 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 638 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 639 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 640 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 641 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 642 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 643 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 644 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 645 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 646 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
| 647 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 648 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 649 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 650 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 651 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 652 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 653 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 654 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 655 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 656 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 657 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 658 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 659 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 660 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 661 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 662 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 663 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 664 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 665 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 666 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 667 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
| 668 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 669 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 670 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 671 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 672 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 673 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 674 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 675 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 676 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 677 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 678 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 679 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 680 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 681 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 682 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
| 683 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 684 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 685 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 686 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 687 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 688 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 689 |
|
|
src/utils/simError.c, src/utils/simError.h, |
| 690 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 691 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 692 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 693 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 694 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 695 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
| 696 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 697 |
tim |
1603 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 698 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 699 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 700 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 701 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 702 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 703 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 704 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 705 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 706 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 707 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 708 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 709 |
|
|
src/applications/LatticeCreator.cpp, |
| 710 |
|
|
src/applications/LatticeCreator.hpp, |
| 711 |
|
|
src/applications/LatticeFactory.cpp, |
| 712 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 713 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 714 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 715 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
| 716 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
| 717 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 718 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 719 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 720 |
|
|
src/applications/simpleBuilder.ggo, |
| 721 |
|
|
src/applications/simpleBuilderCmd.c, |
| 722 |
|
|
src/integrators/AbstractClasses.hpp, |
| 723 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 724 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 725 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 726 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 727 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 728 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 729 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 730 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 731 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 732 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 733 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 734 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 735 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 736 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 737 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 738 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 739 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 740 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 741 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 742 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 743 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 744 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
| 745 |
|
|
samples/argon/500.in, samples/argon/500.md, |
| 746 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 747 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 748 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 749 |
|
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 750 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 751 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 752 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 753 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 754 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 755 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 756 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 757 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 758 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 759 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 760 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 761 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 762 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 763 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 764 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 765 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 766 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 767 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 768 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 769 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 770 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 771 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 772 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 773 |
|
|
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
| 774 |
gezelter |
1490 |
|
| 775 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
| 776 |
gezelter |
1490 |
|
| 777 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 778 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 779 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 780 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 781 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 782 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 783 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 784 |
|
|
src/UseTheForce/fForceField.h, |
| 785 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
| 786 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
| 787 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
| 788 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
| 789 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
| 790 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 791 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
| 792 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 793 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
| 794 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 795 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 796 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 797 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
| 798 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
| 799 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 800 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 801 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
| 802 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
| 803 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 804 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
| 805 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 806 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 807 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 808 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 809 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 810 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 811 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 812 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 813 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 814 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 815 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 816 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 817 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 818 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 819 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 820 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 821 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
| 822 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 823 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 824 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 825 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 826 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 827 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 828 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 829 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 830 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 831 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 832 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 833 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 834 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 835 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 836 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 837 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 838 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 839 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 840 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 841 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 842 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
| 843 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 844 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 845 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 846 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 847 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 848 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 849 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 850 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 851 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 852 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 853 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 854 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 855 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 856 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 857 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
| 858 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 859 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 860 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 861 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 862 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 863 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 864 |
|
|
src/utils/simError.c, src/utils/simError.h, |
| 865 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 866 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 867 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 868 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 869 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 870 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
| 871 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 872 |
tim |
1603 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 873 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 874 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 875 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 876 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 877 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 878 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 879 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 880 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 881 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 882 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 883 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 884 |
|
|
src/applications/LatticeCreator.cpp, |
| 885 |
|
|
src/applications/LatticeCreator.hpp, |
| 886 |
|
|
src/applications/LatticeFactory.cpp, |
| 887 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 888 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 889 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 890 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
| 891 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
| 892 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 893 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 894 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 895 |
|
|
src/applications/simpleBuilder.ggo, |
| 896 |
|
|
src/applications/simpleBuilderCmd.c, |
| 897 |
|
|
src/integrators/AbstractClasses.hpp, |
| 898 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 899 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 900 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 901 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 902 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 903 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 904 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 905 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 906 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 907 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 908 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 909 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 910 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 911 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 912 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 913 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 914 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 915 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 916 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 917 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 918 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 919 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
| 920 |
|
|
samples/argon/500.in, samples/argon/500.md, |
| 921 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 922 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 923 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 924 |
|
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 925 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 926 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 927 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 928 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 929 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 930 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 931 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 932 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 933 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 934 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 935 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 936 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 937 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 938 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 939 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 940 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 941 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 942 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 943 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 944 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 945 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 946 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 947 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 948 |
|
|
forceFields/Pt.VC.funcfl: Initial revision |
| 949 |
gezelter |
1490 |
|
