From e95104ebd155001db8cb9147482a5fac32f3f700 Mon Sep 17 00:00:00 2001 From: Sebastian Kehl Date: Wed, 29 Sep 2021 14:24:53 +0200 Subject: [PATCH] Uncapitalize sc-gapsys parameters in input. --- .../reference-manual/functions/free-energy-interactions.rst | 4 ++-- docs/user-guide/mdp-options.rst | 6 +++--- src/gromacs/gmxpreprocess/readir.cpp | 6 +++--- ...AcceptsDefineParametersWithValuesIncludingAssignment.xml | 6 +++--- .../tests/refdata/GetIrTest_AcceptsElectricField.xml | 6 +++--- .../refdata/GetIrTest_AcceptsElectricFieldOscillating.xml | 6 +++--- .../tests/refdata/GetIrTest_AcceptsElectricFieldPulsed.xml | 6 +++--- .../tests/refdata/GetIrTest_AcceptsEmptyLines.xml | 6 +++--- .../tests/refdata/GetIrTest_AcceptsImplicitSolventNo.xml | 6 +++--- .../tests/refdata/GetIrTest_AcceptsKeyWithoutValue.xml | 6 +++--- .../gmxpreprocess/tests/refdata/GetIrTest_AcceptsMimic.xml | 6 +++--- .../refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml | 6 +++--- src/gromacs/mdtypes/inputrec.cpp | 6 +++--- 13 files changed, 38 insertions(+), 38 deletions(-) diff --git a/docs/reference-manual/functions/free-energy-interactions.rst b/docs/reference-manual/functions/free-energy-interactions.rst index 4b624dd1a0..9ffee3e905 100644 --- a/docs/reference-manual/functions/free-energy-interactions.rst +++ b/docs/reference-manual/functions/free-energy-interactions.rst @@ -338,10 +338,10 @@ the soft-cored non-bonded interactions using the formalism by Gapsys *et al.*\ : The Gapsys *et al.* soft-core is formulated to act on the level of van der Waals and electrostatic forces: the non-bonded interactions are linearized at a point defined as, :math:`r_{scLJ}` or :math:`r_{scQ}`, respectively. The linearization point depends on the state of the system as controlled by the :math:`\lambda` parameter and -two parameters :math:`\alpha_Q` (set with ``sc-gapsys-scale-linpoint-Q``) and :math:`\alpha_{LJ}` (set with ``sc-gapsys-scale-linpoint-LJ``). +two parameters :math:`\alpha_Q` (set with ``sc-gapsys-scale-linpoint-q``) and :math:`\alpha_{LJ}` (set with ``sc-gapsys-scale-linpoint-lj``). The dependence on :math:`\lambda` guarantees that the end-states are properly represented by their hard-core potentials. :numref:`Fig. %s ` illustrates the behaviour of the linearization point, forces and integrated potential energies with respect -to the parameters :math:`\alpha_Q` and :math:`\alpha_{LJ}`. The optimal choices of the parameter values have been systematically explored in :ref:`185 `. These recommended values are set by default when ``sc-function=gapsys`` is selected: ``sc-gapsys-scale-linpoint-Q=0.3`` and ``sc-gapsys-scale-linpoint-LJ=0.85``. +to the parameters :math:`\alpha_Q` and :math:`\alpha_{LJ}`. The optimal choices of the parameter values have been systematically explored in :ref:`185 `. These recommended values are set by default when ``sc-function=gapsys`` is selected: ``sc-gapsys-scale-linpoint-q=0.3`` and ``sc-gapsys-scale-linpoint-lj=0.85``. .. _fig-gapsyssc: diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst index 5077b7db91..e2e0b95688 100644 --- a/docs/user-guide/mdp-options.rst +++ b/docs/user-guide/mdp-options.rst @@ -2584,7 +2584,7 @@ Free energy calculations than :mdp:`sc-sigma`. Used only with `sc-function=beutler` -.. mdp:: sc-gapsys-scale-linpoint-LJ +.. mdp:: sc-gapsys-scale-linpoint-lj (0.85) for `sc-function=gapsys` it is the unitless alphaLJ parameter. @@ -2594,7 +2594,7 @@ Free energy calculations van der Waals interactions. Used only with `sc-function=gapsys` -.. mdp:: sc-gapsys-scale-linpoint-Q +.. mdp:: sc-gapsys-scale-linpoint-q (0.3) [nm/e^2] For `sc-function=gapsys` the alphaQ parameter @@ -2603,7 +2603,7 @@ Free energy calculations result in the standard hard-core Coulombic interactions. Used only with `sc-function=gapsys` -.. mdp:: sc-gapsys-sigma-LJ +.. mdp:: sc-gapsys-sigma-lj (0.3) [nm] for `sc-function=gapsys` the soft-core sigma for particles diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp index 1db9d36ae7..4be0d276fa 100644 --- a/src/gromacs/gmxpreprocess/readir.cpp +++ b/src/gromacs/gmxpreprocess/readir.cpp @@ -2330,9 +2330,9 @@ void get_ir(const char* mdparin, fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi); fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi); fep->bScCoul = (getEnum(&inp, "sc-coul", wi) != Boolean::No); - fep->scGapsysScaleLinpointLJ = get_ereal(&inp, "sc-gapsys-scale-linpoint-LJ", 0.85, wi); - fep->scGapsysScaleLinpointQ = get_ereal(&inp, "sc-gapsys-scale-linpoint-Q", 0.3, wi); - fep->scGapsysSigmaLJ = get_ereal(&inp, "sc-gapsys-sigma-LJ", 0.3, wi); + fep->scGapsysScaleLinpointLJ = get_ereal(&inp, "sc-gapsys-scale-linpoint-lj", 0.85, wi); + fep->scGapsysScaleLinpointQ = get_ereal(&inp, "sc-gapsys-scale-linpoint-q", 0.3, wi); + fep->scGapsysSigmaLJ = get_ereal(&inp, "sc-gapsys-sigma-lj", 0.3, wi); fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi); fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi); fep->separate_dhdl_file = getEnum(&inp, "separate-dhdl-file", wi); diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment.xml index 9641432a59..a7cc35f439 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricField.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricField.xml index bc058c8b9b..cbf5084ddc 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricField.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricField.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldOscillating.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldOscillating.xml index 7c7fcaf4ad..7e439fa8b5 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldOscillating.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldOscillating.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldPulsed.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldPulsed.xml index 89ec917ade..71826f94aa 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldPulsed.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldPulsed.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsEmptyLines.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsEmptyLines.xml index 33b334afaa..d6fc03c7cb 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsEmptyLines.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsEmptyLines.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsImplicitSolventNo.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsImplicitSolventNo.xml index 33b334afaa..d6fc03c7cb 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsImplicitSolventNo.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsImplicitSolventNo.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsKeyWithoutValue.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsKeyWithoutValue.xml index 33b334afaa..d6fc03c7cb 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsKeyWithoutValue.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsKeyWithoutValue.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsMimic.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsMimic.xml index c61ad8c4d1..391a10118c 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsMimic.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsMimic.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml index 7814bd16c2..202eac0de7 100644 --- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml +++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml @@ -255,9 +255,9 @@ sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no -sc-gapsys-scale-linpoint-LJ = 0.85 -sc-gapsys-scale-linpoint-Q = 0.3 -sc-gapsys-sigma-LJ = 0.3 +sc-gapsys-scale-linpoint-lj = 0.85 +sc-gapsys-scale-linpoint-q = 0.3 +sc-gapsys-sigma-lj = 0.3 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 diff --git a/src/gromacs/mdtypes/inputrec.cpp b/src/gromacs/mdtypes/inputrec.cpp index e1efc6756e..9b51dd8ced 100644 --- a/src/gromacs/mdtypes/inputrec.cpp +++ b/src/gromacs/mdtypes/inputrec.cpp @@ -601,9 +601,9 @@ static void pr_fepvals(FILE* fp, int indent, const t_lambda* fep, gmx_bool bMDPf PS("separate-dhdl-file", enumValueToString(fep->separate_dhdl_file)); PS("dhdl-derivatives", enumValueToString(fep->dhdl_derivatives)); PS("sc-function", enumValueToString(fep->softcoreFunction)); - PR("sc-gapsys-scale-linpoint-LJ", fep->scGapsysScaleLinpointLJ); - PR("sc-gapsys-scale-linpoint-Q", fep->scGapsysScaleLinpointQ); - PR("sc-gapsys-sigma-LJ", fep->scGapsysSigmaLJ); + PR("sc-gapsys-scale-linpoint-lj", fep->scGapsysScaleLinpointLJ); + PR("sc-gapsys-scale-linpoint-q", fep->scGapsysScaleLinpointQ); + PR("sc-gapsys-sigma-lj", fep->scGapsysSigmaLJ); }; static void pr_pull(FILE* fp, int indent, const pull_params_t& pull) -- 2.22.0