Unverified Commit f7e214ee authored by Jacob Gissinger's avatar Jacob Gissinger Committed by GitHub
Browse files

Merge pull request #63 from lammps/master 

rebase
parents f5fb9f20 402f5585

cmake/Modules/Packages/KIM.cmake

+10 −0
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@@ -5,6 +5,16 @@ if(PKG_KIM) 
    include_directories(${CURL_INCLUDE_DIRS})

    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})

    add_definitions(-DLMP_KIM_CURL)

    set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")

    mark_as_advanced(LMP_DEBUG_CURL)

    if(LMP_DEBUG_CURL)

      add_definitions(-DLMP_DEBUG_CURL)

    endif()

    set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")

    mark_as_advanced(LMP_NO_SSL_CHECK)

    if(LMP_NO_SSL_CHECK)

      add_definitions(-DLMP_NO_SSL_CHECK)

    endif()

  endif()

  find_package(KIM-API QUIET)

  if(KIM-API_FOUND)

doc/src/.gitignore

+3 −2
Original line number Diff line number Diff line 
Eqs

JPG
 
/Eqs

/JPG

/false_positives.txt

doc/src/Build_extras.rst

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@@ -195,12 +195,32 @@ minutes to hours) to build. Of course you only need to do that once.) 
.. parsed-literal::



   -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes

   -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on

   -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes



If DOWNLOAD\_KIM is set, the KIM library will be downloaded and built

inside the CMake build directory.  If the KIM library is already on

your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH

environment variable so that libkim-api can be found.



For using KIM web queries.



If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any

libcurl calls within the KIM web query display a lot of information about

libcurl operations. You hardly ever want this set in production use, you will

almost always want this when you debug/report problems.



The libcurl performs peer SSL certificate verification by default. This

verification is done using a CA certificate store that the SSL library can

use to make sure the peer's server certificate is valid. If SSL reports an

error ("certificate verify failed") during the handshake and thus refuses

further communication with that server, you can set LMP\_NO\_SSL\_CHECK.

If LMP\_NO\_SSL\_CHECK is set, libcurl does not verify the peer and connection

succeeds regardless of the names in the certificate. This option is insecure.

As an alternative, you can specify your own CA cert path by setting the

environment variable CURL\_CA\_BUNDLE to the path of your choice. A call to the

KIM web query would get this value from the environmental variable.



**Traditional make**\ :



You can download and build the KIM library manually if you prefer;

doc/src/Commands.rst

+0 −5
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@@ -27,8 +27,3 @@ commands in it are used to define a LAMMPS simulation. 
   :maxdepth: 1



   Commands_removed
 




.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Commands_all.html

doc/src/Commands_all.rst

+128 −52
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+----------------------------------------+------------------------------------+------------------------------------------+

| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |

+----------------------------------------+------------------------------------+------------------------------------------+

| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |

+----------------------------------------+------------------------------------+------------------------------------------+

| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |

+----------------------------------------+------------------------------------+------------------------------------------+

.. table_from_list::

   :columns: 3



   * :doc:`General commands <Commands_all>`

   * :doc:`Fix styles <Commands_fix>`

   * :doc:`Compute styles <Commands_compute>`

   * :doc:`Pair styles <Commands_pair>`

   * :ref:`Bond styles <bond>`

   * :ref:`Angle styles <angle>`

   * :ref:`Dihedral styles <dihedral>`

   * :ref:`Improper styles <improper>`

   * :doc:`KSpace styles <Commands_kspace>`



General commands

================



An alphabetic list of all general LAMMPS commands.



+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`angle\_coeff <angle_coeff>`       | :doc:`angle\_style <angle_style>`       | :doc:`atom\_modify <atom_modify>`       | :doc:`atom\_style <atom_style>`         | :doc:`balance <balance>`                    | :doc:`bond\_coeff <bond_coeff>`         |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`bond\_style <bond_style>`         | :doc:`bond\_write <bond_write>`         | :doc:`boundary <boundary>`              | :doc:`box <box>`                        | :doc:`change\_box <change_box>`             | :doc:`clear <clear>`                    |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`comm\_modify <comm_modify>`       | :doc:`comm\_style <comm_style>`         | :doc:`compute <compute>`                | :doc:`compute\_modify <compute_modify>` | :doc:`create\_atoms <create_atoms>`         | :doc:`create\_bonds <create_bonds>`     |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`create\_box <create_box>`         | :doc:`delete\_atoms <delete_atoms>`     | :doc:`delete\_bonds <delete_bonds>`     | :doc:`dielectric <dielectric>`          | :doc:`dihedral\_coeff <dihedral_coeff>`     | :doc:`dihedral\_style <dihedral_style>` |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`dimension <dimension>`            | :doc:`displace\_atoms <displace_atoms>` | :doc:`dump <dump>`                      | :doc:`dump adios <dump_adios>`          | :doc:`dump image <dump_image>`              | :doc:`dump movie <dump_image>`          |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`dump netcdf <dump_netcdf>`        | :doc:`dump netcdf/mpiio <dump_netcdf>`  | :doc:`dump vtk <dump_vtk>`              | :doc:`dump\_modify <dump_modify>`       | :doc:`dynamical\_matrix <dynamical_matrix>` | :doc:`echo <echo>`                      |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`fix <fix>`                        | :doc:`fix\_modify <fix_modify>`         | :doc:`group <group>`                    | :doc:`group2ndx <group2ndx>`            | :doc:`hyper <hyper>`                        | :doc:`if <if>`                          |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`info <info>`                      | :doc:`improper\_coeff <improper_coeff>` | :doc:`improper\_style <improper_style>` | :doc:`include <include>`                | :doc:`jump <jump>`                          | :doc:`kim\_init <kim_commands>`         |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`kim\_interactions <kim_commands>` | :doc:`kim\_query <kim_commands>`        | :doc:`kspace\_modify <kspace_modify>`   | :doc:`kspace\_style <kspace_style>`     | :doc:`label <label>`                        | :doc:`lattice <lattice>`                |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`log <log>`                        | :doc:`mass <mass>`                      | :doc:`message <message>`                | :doc:`minimize <minimize>`              | :doc:`min\_modify <min_modify>`             | :doc:`min\_style <min_style>`           |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`min\_style spin <min_spin>`       | :doc:`molecule <molecule>`              | :doc:`ndx2group <group2ndx>`            | :doc:`neb <neb>`                        | :doc:`neb/spin <neb_spin>`                  | :doc:`neigh\_modify <neigh_modify>`     |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`neighbor <neighbor>`              | :doc:`newton <newton>`                  | :doc:`next <next>`                      | :doc:`package <package>`                | :doc:`pair\_coeff <pair_coeff>`             | :doc:`pair\_modify <pair_modify>`       |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`pair\_style <pair_style>`         | :doc:`pair\_write <pair_write>`         | :doc:`partition <partition>`            | :doc:`prd <prd>`                        | :doc:`print <print>`                        | :doc:`processors <processors>`          |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`python <python>`                  | :doc:`quit <quit>`                      | :doc:`read\_data <read_data>`           | :doc:`read\_dump <read_dump>`           | :doc:`read\_restart <read_restart>`         | :doc:`region <region>`                  |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`replicate <replicate>`            | :doc:`rerun <rerun>`                    | :doc:`reset\_ids <reset_ids>`           | :doc:`reset\_timestep <reset_timestep>` | :doc:`restart <restart>`                    | :doc:`run <run>`                        |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`run\_style <run_style>`           | :doc:`server <server>`                  | :doc:`set <set>`                        | :doc:`shell <shell>`                    | :doc:`special\_bonds <special_bonds>`       | :doc:`suffix <suffix>`                  |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`tad <tad>`                        | :doc:`temper <temper>`                  | :doc:`temper/grem <temper_grem>`        | :doc:`temper/npt <temper_npt>`          | :doc:`thermo <thermo>`                      | :doc:`thermo\_modify <thermo_modify>`   |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`thermo\_style <thermo_style>`     | :doc:`third\_order <third_order>`       | :doc:`timer <timer>`                    | :doc:`timestep <timestep>`              | :doc:`uncompute <uncompute>`                | :doc:`undump <undump>`                  |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`unfix <unfix>`                    | :doc:`units <units>`                    | :doc:`variable <variable>`              | :doc:`velocity <velocity>`              | :doc:`write\_coeff <write_coeff>`           | :doc:`write\_data <write_data>`         |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+

| :doc:`write\_dump <write_dump>`         | :doc:`write\_restart <write_restart>`   |                                         |                                         |                                             |                                         |

+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+



.. table_from_list::

   :columns: 6



.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Commands_all.html
 
   * :doc:`angle_coeff <angle_coeff>`

   * :doc:`angle_style <angle_style>`

   * :doc:`atom_modify <atom_modify>`

   * :doc:`atom_style <atom_style>`

   * :doc:`balance <balance>`

   * :doc:`bond_coeff <bond_coeff>`

   * :doc:`bond\_style <bond_style>`

   * :doc:`bond\_write <bond_write>`

   * :doc:`boundary <boundary>`

   * :doc:`box <box>`

   * :doc:`change\_box <change_box>`

   * :doc:`clear <clear>`

   * :doc:`comm\_modify <comm_modify>`

   * :doc:`comm\_style <comm_style>`

   * :doc:`compute <compute>`

   * :doc:`compute\_modify <compute_modify>`

   * :doc:`create\_atoms <create_atoms>`

   * :doc:`create\_bonds <create_bonds>`

   * :doc:`create\_box <create_box>`

   * :doc:`delete\_atoms <delete_atoms>`

   * :doc:`delete\_bonds <delete_bonds>`

   * :doc:`dielectric <dielectric>`

   * :doc:`dihedral\_coeff <dihedral_coeff>`

   * :doc:`dihedral\_style <dihedral_style>`

   * :doc:`dimension <dimension>`

   * :doc:`displace\_atoms <displace_atoms>`

   * :doc:`dump <dump>`

   * :doc:`dump adios <dump_adios>`

   * :doc:`dump image <dump_image>`

   * :doc:`dump movie <dump_image>`

   * :doc:`dump netcdf <dump_netcdf>`

   * :doc:`dump netcdf/mpiio <dump_netcdf>`

   * :doc:`dump vtk <dump_vtk>`

   * :doc:`dump\_modify <dump_modify>`

   * :doc:`dynamical\_matrix <dynamical_matrix>`

   * :doc:`echo <echo>`

   * :doc:`fix <fix>`

   * :doc:`fix\_modify <fix_modify>`

   * :doc:`group <group>`

   * :doc:`group2ndx <group2ndx>`

   * :doc:`hyper <hyper>`

   * :doc:`if <if>`

   * :doc:`improper\_coeff <improper_coeff>`

   * :doc:`improper\_style <improper_style>`

   * :doc:`include <include>`

   * :doc:`jump <jump>`

   * :doc:`kim\_init <kim_commands>`

   * :doc:`kim\_interactions <kim_commands>`

   * :doc:`kim\_query <kim_commands>`

   * :doc:`kspace\_modify <kspace_modify>`

   * :doc:`kspace\_style <kspace_style>`

   * :doc:`label <label>`

   * :doc:`lattice <lattice>`

   * :doc:`log <log>`

   * :doc:`mass <mass>`

   * :doc:`message <message>`

   * :doc:`minimize <minimize>`

   * :doc:`min\_modify <min_modify>`

   * :doc:`min\_style <min_style>`

   * :doc:`min\_style spin <min_spin>`

   * :doc:`molecule <molecule>`

   * :doc:`ndx2group <group2ndx>`

   * :doc:`neb <neb>`

   * :doc:`neb/spin <neb_spin>`

   * :doc:`neigh\_modify <neigh_modify>`

   * :doc:`neighbor <neighbor>`

   * :doc:`newton <newton>`

   * :doc:`next <next>`

   * :doc:`package <package>`

   * :doc:`pair\_coeff <pair_coeff>`

   * :doc:`pair\_modify <pair_modify>`

   * :doc:`pair\_write <pair_write>`

   * :doc:`partition <partition>`

   * :doc:`prd <prd>`

   * :doc:`print <print>`

   * :doc:`processors <processors>`

   * :doc:`python <python>`

   * :doc:`quit <quit>`

   * :doc:`read\_data <read_data>`

   * :doc:`read\_dump <read_dump>`

   * :doc:`read\_restart <read_restart>`

   * :doc:`region <region>`

   * :doc:`replicate <replicate>`

   * :doc:`rerun <rerun>`

   * :doc:`reset\_ids <reset_ids>`

   * :doc:`reset\_timestep <reset_timestep>`

   * :doc:`restart <restart>`

   * :doc:`run <run>`

   * :doc:`run\_style <run_style>`

   * :doc:`server <server>`

   * :doc:`set <set>`

   * :doc:`shell <shell>`

   * :doc:`special\_bonds <special_bonds>`

   * :doc:`suffix <suffix>`

   * :doc:`tad <tad>`

   * :doc:`temper <temper>`

   * :doc:`temper/grem <temper_grem>`

   * :doc:`temper/npt <temper_npt>`

   * :doc:`thermo <thermo>`

   * :doc:`thermo\_modify <thermo_modify>`

   * :doc:`thermo\_style <thermo_style>`

   * :doc:`third\_order <third_order>`

   * :doc:`timer <timer>`

   * :doc:`timestep <timestep>`

   * :doc:`uncompute <uncompute>`

   * :doc:`undump <undump>`

   * :doc:`unfix <unfix>`

   * :doc:`units <units>`

   * :doc:`variable <variable>`

   * :doc:`velocity <velocity>`

   * :doc:`write\_coeff <write_coeff>`

   * :doc:`write\_data <write_data>`

   * :doc:`write\_dump <write_dump>`

   * :doc:`write\_restart <write_restart>`

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