Loading doc/src/Section_errors.txt +4 −4 Original line number Diff line number Diff line Loading @@ -11351,19 +11351,19 @@ have fully consistent image flags, since some bonds will cross periodic boundaries and connect two atoms with the same image flag. :dd {KIM Model does not provide `energy'; Potential energy will be zero} :dt {KIM Model does not provide 'energy'; Potential energy will be zero} :dt Self-explanatory. :dd {KIM Model does not provide `forces'; Forces will be zero} :dt {KIM Model does not provide 'forces'; Forces will be zero} :dt Self-explanatory. :dd {KIM Model does not provide `particleEnergy'; energy per atom will be zero} :dt {KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt Self-explanatory. :dd {KIM Model does not provide `particleVirial'; virial per atom will be zero} :dt {KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt Self-explanatory. :dd Loading doc/src/Section_start.txt +2 −2 Original line number Diff line number Diff line Loading @@ -1080,12 +1080,12 @@ Here is an example of such errors when the system FFTW or provided lib/colvars library have not been built as shared libraries: /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared R_X86_64_32 against '.rodata' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o): relocation R_X86_64_32 against `__pthread_key_create' can not be used relocation R_X86_64_32 against '__pthread_key_create' can not be used when making a shared object; recompile with -fPIC ../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre Loading doc/src/tutorial_github.txt +5 −5 Original line number Diff line number Diff line Loading @@ -22,7 +22,7 @@ book"_http://git-scm.com/book/ to reacquaint yourself. First of all, you need a GitHub account. This is fairly simple, just go to "GitHub"_https://github.com and create an account by clicking the ``Sign up for GitHub'' button. Once your account is created, you the "Sign up for GitHub" button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password. Loading @@ -33,7 +33,7 @@ username or e-mail address and password. To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS on GitHub"_https://github.com/lammps/lammps and make sure branch is set to ``lammps-icms'', see the figure below. set to "lammps-icms", see the figure below. :c,image(JPG/tutorial_branch.png) Loading @@ -58,7 +58,7 @@ will contain these changes, a so-called feature branch. Since LAMMPS is such a big project and most user contributions come in small portions, the most ideal workflow for LAMMPS is the so-called ``Feature branch'' workflow. It is explained in great detail here: "Feature branch" workflow. It is explained in great detail here: "feature branch workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow. Loading @@ -78,7 +78,7 @@ You can find the proper url to the right of the "HTTPS" block, see figure. :c,image(JPG/tutorial_https_block.png) The above command copies (``clones'') the git repository to your local The above command copies ("clones") the git repository to your local machine. You can use this local clone to make changes and test them without interfering with the repository on github. First, however, it is recommended to make a new branch for a particular feature you would Loading @@ -101,7 +101,7 @@ you should switch branches! After everything is done, add the files to the branch and commit them: $ git add src/USER-MANIFOLD examples/USER/manifold/ $ git add doc/fix_nv{t,e}_manifold_rattle.txt $ git add doc/fix_nv\{t,e\}_manifold_rattle.txt $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre After the files are added, the change should be comitted: Loading src/KIM/pair_kim.h +4 −4 Original line number Diff line number Diff line Loading @@ -197,19 +197,19 @@ E: Unknown unit_style Self-explanatory. Check the input script or data file. W: KIM Model does not provide `energy'; Potential energy will be zero W: KIM Model does not provide 'energy'; Potential energy will be zero Self-explanatory. W: KIM Model does not provide `forces'; Forces will be zero W: KIM Model does not provide 'forces'; Forces will be zero Self-explanatory. W: KIM Model does not provide `particleEnergy'; energy per atom will be zero W: KIM Model does not provide 'particleEnergy'; energy per atom will be zero Self-explanatory. W: KIM Model does not provide `particleVirial'; virial per atom will be zero W: KIM Model does not provide 'particleVirial'; virial per atom will be zero Self-explanatory. Loading Loading
doc/src/Section_errors.txt +4 −4 Original line number Diff line number Diff line Loading @@ -11351,19 +11351,19 @@ have fully consistent image flags, since some bonds will cross periodic boundaries and connect two atoms with the same image flag. :dd {KIM Model does not provide `energy'; Potential energy will be zero} :dt {KIM Model does not provide 'energy'; Potential energy will be zero} :dt Self-explanatory. :dd {KIM Model does not provide `forces'; Forces will be zero} :dt {KIM Model does not provide 'forces'; Forces will be zero} :dt Self-explanatory. :dd {KIM Model does not provide `particleEnergy'; energy per atom will be zero} :dt {KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt Self-explanatory. :dd {KIM Model does not provide `particleVirial'; virial per atom will be zero} :dt {KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt Self-explanatory. :dd Loading
doc/src/Section_start.txt +2 −2 Original line number Diff line number Diff line Loading @@ -1080,12 +1080,12 @@ Here is an example of such errors when the system FFTW or provided lib/colvars library have not been built as shared libraries: /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared R_X86_64_32 against '.rodata' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o): relocation R_X86_64_32 against `__pthread_key_create' can not be used relocation R_X86_64_32 against '__pthread_key_create' can not be used when making a shared object; recompile with -fPIC ../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre Loading
doc/src/tutorial_github.txt +5 −5 Original line number Diff line number Diff line Loading @@ -22,7 +22,7 @@ book"_http://git-scm.com/book/ to reacquaint yourself. First of all, you need a GitHub account. This is fairly simple, just go to "GitHub"_https://github.com and create an account by clicking the ``Sign up for GitHub'' button. Once your account is created, you the "Sign up for GitHub" button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password. Loading @@ -33,7 +33,7 @@ username or e-mail address and password. To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS on GitHub"_https://github.com/lammps/lammps and make sure branch is set to ``lammps-icms'', see the figure below. set to "lammps-icms", see the figure below. :c,image(JPG/tutorial_branch.png) Loading @@ -58,7 +58,7 @@ will contain these changes, a so-called feature branch. Since LAMMPS is such a big project and most user contributions come in small portions, the most ideal workflow for LAMMPS is the so-called ``Feature branch'' workflow. It is explained in great detail here: "Feature branch" workflow. It is explained in great detail here: "feature branch workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow. Loading @@ -78,7 +78,7 @@ You can find the proper url to the right of the "HTTPS" block, see figure. :c,image(JPG/tutorial_https_block.png) The above command copies (``clones'') the git repository to your local The above command copies ("clones") the git repository to your local machine. You can use this local clone to make changes and test them without interfering with the repository on github. First, however, it is recommended to make a new branch for a particular feature you would Loading @@ -101,7 +101,7 @@ you should switch branches! After everything is done, add the files to the branch and commit them: $ git add src/USER-MANIFOLD examples/USER/manifold/ $ git add doc/fix_nv{t,e}_manifold_rattle.txt $ git add doc/fix_nv\{t,e\}_manifold_rattle.txt $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre After the files are added, the change should be comitted: Loading
src/KIM/pair_kim.h +4 −4 Original line number Diff line number Diff line Loading @@ -197,19 +197,19 @@ E: Unknown unit_style Self-explanatory. Check the input script or data file. W: KIM Model does not provide `energy'; Potential energy will be zero W: KIM Model does not provide 'energy'; Potential energy will be zero Self-explanatory. W: KIM Model does not provide `forces'; Forces will be zero W: KIM Model does not provide 'forces'; Forces will be zero Self-explanatory. W: KIM Model does not provide `particleEnergy'; energy per atom will be zero W: KIM Model does not provide 'particleEnergy'; energy per atom will be zero Self-explanatory. W: KIM Model does not provide `particleVirial'; virial per atom will be zero W: KIM Model does not provide 'particleVirial'; virial per atom will be zero Self-explanatory. Loading
