From 734bc915e28c3c57ba19910fa295ca0ffe8f7b2f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 14:14:20 -0400 Subject: [PATCH 1/8] must include third_party folder with legacy build --- src/Makefile.package.empty | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makefile.package.empty b/src/Makefile.package.empty index 24e4c76bea..559f387981 100644 --- a/src/Makefile.package.empty +++ b/src/Makefile.package.empty @@ -7,6 +7,6 @@ PKG_LIB = PKG_CPP_DEPENDS = PKG_LINK_DEPENDS = -PKG_SYSINC = +PKG_SYSINC = -I ../../third_party PKG_SYSLIB = PKG_SYSPATH = From cab78b2c0dc70513aa575d7ea65afcfdd8de7a61 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 14:15:01 -0400 Subject: [PATCH 2/8] correct docs related to adding explicit Coulomb interactions --- doc/src/pair_lj_pirani.rst | 49 ++++++++++++++++++-------------------- 1 file changed, 23 insertions(+), 26 deletions(-) diff --git a/doc/src/pair_lj_pirani.rst b/doc/src/pair_lj_pirani.rst index 7a28f280a7..abf57b87ce 100644 --- a/doc/src/pair_lj_pirani.rst +++ b/doc/src/pair_lj_pirani.rst @@ -50,16 +50,16 @@ Lennard-Jones (LJ) formulation is usually applied. :math:`r_c` is the cutoff. -An additional parameter, :math:`\alpha`, has been introduced in order -to be able to recover the traditional Lennard-Jones 12-6 with a specific -choice of parameters. With :math:`R_m \equiv r_0 = \sigma \cdot 2^{1 / 6}`, -:math:`\alpha = 0`, :math:`\beta = 12` and :math:`\gamma = 6` -it is straightforward to prove that LJ 12-6 is obtained. Also, it can be +An additional parameter, :math:`\alpha`, has been introduced in order to +be able to recover the traditional Lennard-Jones 12-6 with a specific +choice of parameters. With :math:`R_m \equiv r_0 = \sigma \cdot 2^{1 / +6}`, :math:`\alpha = 0`, :math:`\beta = 12` and :math:`\gamma = 6` it is +straightforward to prove that LJ 12-6 is obtained. Also, it can be verified that using :math:`\alpha= 4`, :math:`\beta= 8` and :math:`\gamma = 6`, at the equilibrium distance, the first and second derivatives of ILJ match those of LJ 12-6. The parameter :math:`R_m` -corresponds to the equilibrium distance and :math:`\epsilon` to the -well depth. +corresponds to the equilibrium distance and :math:`\epsilon` to the well +depth. This potential provides some advantages with respect to the standard LJ @@ -67,28 +67,25 @@ potential, as explained in :ref:`(Pirani) `: it provides a more realistic description of the long range behaviour and an attenuation of the hardness of the repulsive wall. - This force field can be used for neutral-neutral (:math:`\gamma = 6`), -ion-neutral (:math:`\gamma = 4`) or ion-ion systems (:math:`\gamma = 1`). -Notice that this implementation does not include explicit electrostatic -interactions. If these are desired, this pair style should be used along -with a Coulomb pair style :doc:`pair_style coul/cut ` and -optional long-range Coulombics, which can be done using the pair style -hybrid :doc:`pair_style hybrid ` and kspace -style :doc:`kspace_style ` commands. +ion-neutral (:math:`\gamma = 4`) or ion-ion systems (:math:`\gamma = +1`). Notice that this implementation does not include explicit +electrostatic interactions. If these are desired, this pair style +should be used along with a Coulomb pair style like +:doc:`pair styles coul/cut or coul/long ` by using +:doc:`pair style hybrid/overlay ` and a suitable +kspace style :doc:``, if needed. - -As discussed in :ref:`(Pirani) `, analyses of a -variety of systems showed that :math:`\alpha= 4` generally works very well. -In some special cases (e.g. those involving very small multiple charged ions) -this factor may take a slightly different value. The parameter +As discussed in :ref:`(Pirani) `, analysis of a variety of +systems showed that :math:`\alpha= 4` generally works very well. In +some special cases (e.g. those involving very small multiple charged +ions) this factor may take a slightly different value. The parameter :math:`\beta` codifies the hardness (polarizability) of the interacting -partners, and for neutral-neutral systems it usually ranges from 6 to 11. -Moreover, the modulation of :math:`\beta` can model additional interaction -effects, such as charge transfer in the perturbative limit, and can -mitigate the effect of some uncertainty in the data used to build up -the potential function. - +partners, and for neutral-neutral systems it usually ranges from 6 +to 11. Moreover, the modulation of :math:`\beta` can model additional +interaction effects, such as charge transfer in the perturbative limit, +and can mitigate the effect of some uncertainty in the data used to +build up the potential function. The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples From 3b9ddf7a1f0d54524f13b09268f813f8275632a5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 14:59:42 -0400 Subject: [PATCH 3/8] spelling --- doc/src/pair_lj_pirani.rst | 2 +- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/pair_lj_pirani.rst b/doc/src/pair_lj_pirani.rst index abf57b87ce..c7f2703c01 100644 --- a/doc/src/pair_lj_pirani.rst +++ b/doc/src/pair_lj_pirani.rst @@ -64,7 +64,7 @@ depth. This potential provides some advantages with respect to the standard LJ potential, as explained in :ref:`(Pirani) `: it provides a more -realistic description of the long range behaviour and an attenuation of +realistic description of the long range behavior and an attenuation of the hardness of the repulsive wall. This force field can be used for neutral-neutral (:math:`\gamma = 6`), diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 2a774e4993..cf90ce802d 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2965,6 +2965,7 @@ Piola pIp pipelining Pirani +pirani Pisarev Pishevar Pitera From c8b841b08e5937df2ee4e3c7d59d4853d0558c65 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 15:31:32 -0400 Subject: [PATCH 4/8] small tweak --- src/Makefile.package.empty | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makefile.package.empty b/src/Makefile.package.empty index 559f387981..6048b88029 100644 --- a/src/Makefile.package.empty +++ b/src/Makefile.package.empty @@ -7,6 +7,6 @@ PKG_LIB = PKG_CPP_DEPENDS = PKG_LINK_DEPENDS = -PKG_SYSINC = -I ../../third_party +PKG_SYSINC = -I../../third_party PKG_SYSLIB = PKG_SYSPATH = From 15970194195b11ef28b4e55e4459ac4cadf10d6c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 15:44:52 -0400 Subject: [PATCH 5/8] another small tweak --- src/json.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/json.h b/src/json.h index 2f364b445e..4a48aa9c5c 100644 --- a/src/json.h +++ b/src/json.h @@ -17,7 +17,7 @@ // wrapper around including the JSON parsing and writing class // Do NOT include in any header file -#include "nlohmann/json.hpp" +#include namespace LAMMPS_NS { using json = ::nlohmann_lmp::json; From 9b258d4c82f30d98ed1e243c16d4c906ebb162df Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 15:51:39 -0400 Subject: [PATCH 6/8] try another variant --- src/Makefile.package.empty | 2 +- src/json.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Makefile.package.empty b/src/Makefile.package.empty index 6048b88029..b5693af293 100644 --- a/src/Makefile.package.empty +++ b/src/Makefile.package.empty @@ -7,6 +7,6 @@ PKG_LIB = PKG_CPP_DEPENDS = PKG_LINK_DEPENDS = -PKG_SYSINC = -I../../third_party +PKG_SYSINC = -I../../third_party -I../third_party PKG_SYSLIB = PKG_SYSPATH = diff --git a/src/json.h b/src/json.h index 4a48aa9c5c..2f364b445e 100644 --- a/src/json.h +++ b/src/json.h @@ -17,7 +17,7 @@ // wrapper around including the JSON parsing and writing class // Do NOT include in any header file -#include +#include "nlohmann/json.hpp" namespace LAMMPS_NS { using json = ::nlohmann_lmp::json; From 46f4f5a3c06cbaa223386459ecc6758e96698c07 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 16:11:11 -0400 Subject: [PATCH 7/8] move JSON class back to try recover legacy builds --- src/Makefile.package.empty | 2 +- {third_party => src}/nlohmann/json.hpp | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename {third_party => src}/nlohmann/json.hpp (100%) diff --git a/src/Makefile.package.empty b/src/Makefile.package.empty index b5693af293..0e2c8ad915 100644 --- a/src/Makefile.package.empty +++ b/src/Makefile.package.empty @@ -7,6 +7,6 @@ PKG_LIB = PKG_CPP_DEPENDS = PKG_LINK_DEPENDS = -PKG_SYSINC = -I../../third_party -I../third_party +PKG_SYSINC = PKG_SYSLIB = PKG_SYSPATH = diff --git a/third_party/nlohmann/json.hpp b/src/nlohmann/json.hpp similarity index 100% rename from third_party/nlohmann/json.hpp rename to src/nlohmann/json.hpp From d416202b71e371a1e07ac16354b486bc5aeab707 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 25 Apr 2025 16:16:15 -0400 Subject: [PATCH 8/8] restore missing blank --- src/Makefile.package.empty | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makefile.package.empty b/src/Makefile.package.empty index 0e2c8ad915..24e4c76bea 100644 --- a/src/Makefile.package.empty +++ b/src/Makefile.package.empty @@ -7,6 +7,6 @@ PKG_LIB = PKG_CPP_DEPENDS = PKG_LINK_DEPENDS = -PKG_SYSINC = +PKG_SYSINC = PKG_SYSLIB = PKG_SYSPATH =