Uncapitalize sc-gapsys parameters in input.

diff --git a/docs/reference-manual/functions/free-energy-interactions.rst b/docs/reference-manual/functions/free-energy-interactions.rst
index 4b624dd1a0af63fc4b62d2f7a3fbe808c3affb3d..9ffee3e90546898c7f93ebf1cccf41c713a2eb22 100644 (file)
--- 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 <fig-gapsyssc>` 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 <refGapsys2012>`. 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 <refGapsys2012>`. 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 5077b7db9180aced2378a47a607f69487e440c86..e2e0b9568865ab2805767edb936e241506c91e09 100644 (file)
--- 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 1db9d36ae7d3cbf2a2bcd9fc0d5dff6198fee4b5..4be0d276faac84cdc00914702a01b71d93fa5544 100644 (file)
--- 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<Boolean>(&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<SeparateDhdlFile>(&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 9641432a595dd479ba37797c34a3998c5d62a647..a7cc35f439494cb71a6eac5ccdf50193d87afe82 100644 (file)
--- 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 bc058c8b9bb9577614a932c433f9cd3131769149..cbf5084ddc1e8688f3b8ebfc4da981306c7b124c 100644 (file)
--- 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 7c7fcaf4ad068171b6313c4865c038b56b0eee36..7e439fa8b5fb80babed83e495fc003e9d13d2970 100644 (file)
--- 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 89ec917ade8befff90abec372e6e3c65ab7e40e9..71826f94aa694cff9c4068ea18639038d7c5a5e0 100644 (file)
--- 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 33b334afaadae25af5a47095ce4f9aa3a4ac039c..d6fc03c7cbe2e66b420c91792f76e441535bacd1 100644 (file)
--- 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 33b334afaadae25af5a47095ce4f9aa3a4ac039c..d6fc03c7cbe2e66b420c91792f76e441535bacd1 100644 (file)
--- 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 33b334afaadae25af5a47095ce4f9aa3a4ac039c..d6fc03c7cbe2e66b420c91792f76e441535bacd1 100644 (file)
--- 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 c61ad8c4d12eeaaf7bcaca0c3000dc3adfa864b2..391a10118cdd1b97e4070ac2786e2f19a1b182cd 100644 (file)
--- 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 7814bd16c2302a8a6ab004a1623f1e2458c35636..202eac0de7cb7a2d89aba7edd219c78eb7548629 100644 (file)
--- 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 e1efc6756e4461b33ccc6411362072046f4fd8d8..9b51dd8cedb9c118821a34423edfd3edec85a2bf 100644 (file)
--- 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)