diff --git a/doc/Makefile b/doc/Makefile index 1876ad4..5dc2f63 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -48,6 +48,9 @@ clean: html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo + mkdir -p _static/water _static/benzene + cp ../share/validation/water/trajectory-*.png _static/water/. + cp ../share/validation/benzene/trajectory-*.png _static/benzene/. @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." dirhtml: diff --git a/doc/vl.rst b/doc/vl.rst index 328ec67..4bacb6d 100644 --- a/doc/vl.rst +++ b/doc/vl.rst @@ -64,7 +64,7 @@ Finally, two validations are performed for each system: .. _seclab_vl_water: -Validation 1 - Water +Validation 1 - water ********************** Force field construction @@ -124,21 +124,21 @@ trajectories, two bonds and one bend. * **First O-H bond**: -.. image:: ../../../share/validation/water/trajectory-BondHarm-H.O-0_Ehc3.png +.. image:: ../../_static/water/trajectory-BondHarm-H.O-0_Ehc3.png :width: 400 - :target: ../../../share/validation/water/trajectory-BondHarm-H.O-0_Ehc3.png + :target: ../../_static/water/trajectory-BondHarm-H.O-0_Ehc3.png * **Second O-H bond**: -.. image:: ../../../share/validation/water/trajectory-BondHarm-H.O-1_Ehc3.png +.. image:: ../../_static/water/trajectory-BondHarm-H.O-1_Ehc3.png :width: 400 - :target: ../../../share/validation/water/trajectory-BondHarm-H.O-1_Ehc3.png + :target: ../../_static/water/trajectory-BondHarm-H.O-1_Ehc3.png * **H-O-H bend**: -.. image:: ../../../share/validation/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png +.. image:: ../../_static/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png :width: 400 - :target: ../../../share/validation/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png + :target: ../../_static/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png Geometry and frequencies @@ -149,9 +149,9 @@ Geometry and frequencies | -.. _seclab_vl_benzene: +.. _seclab_vl__static/benzene: -Validation 2 - Benzene +Validation 2 - benzene ********************** Force field construction @@ -211,137 +211,137 @@ trajectories, two bonds and one bend. * **C-H bonds**: -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-0_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-0_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-0_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.H-0_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-7_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-7_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-7_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.H-7_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-8_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-8_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-8_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.H-8_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-9_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-9_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-9_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.H-9_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-10_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-10_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-10_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.H-10_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-11_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-11_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-11_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.H-11_Ehc3.png * **C-C bonds**: -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-1_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-1_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-1_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.C-1_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-2_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-2_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-2_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.C-2_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-3_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-3_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-3_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.C-3_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-4_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-4_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-4_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.C-4_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-5_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-5_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-5_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.C-5_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-6_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-6_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-6_Ehc3.png + :target: ../../_static/benzene/trajectory-BondHarm-C.C-6_Ehc3.png * **C-C-C bends**: -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png * **C-C-H bends**: -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png +.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png + :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png * **C-C-H-C out-of-plane distances**: -.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png +.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png + :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png +.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png + :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png +.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png + :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png +.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png + :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png +.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png + :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png -.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png +.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png :width: 400 - :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png + :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png Geometry and frequencies diff --git a/quickff/perturbation.py b/quickff/perturbation.py index ceb5ea8..8479134 100644 --- a/quickff/perturbation.py +++ b/quickff/perturbation.py @@ -378,15 +378,15 @@ def estimate(self, trajectory, ai, ffrefs=[], do_valence=False, energy_noise=Non do_valence If set to True, the current valence force field (stored in self.valence) will be used to compute the valence contribution - + energy_noise - If set to a float, the parabolic fitting will be repeated + If set to a float, the parabolic fitting will be repeated Nerrorsteps times including normal noise on top of the reference - value. The mean of the noise is 0, while the std equals the - number given by energy_noise. The resulting fits give a - distribution of force constants and rest values instead of - single value, the std is used to identify bad estimates, the - mean is used for the actual FF parametrs. If set to nan, the + value. The mean of the noise is 0, while the std equals the + number given by energy_noise. The resulting fits give a + distribution of force constants and rest values instead of + single value, the std is used to identify bad estimates, the + mean is used for the actual FF parametrs. If set to nan, the parabolic fit is performed only once without any noise. ''' with log.section('PTEST', 3, timer='PT Estimate'): diff --git a/quickff/tools.py b/quickff/tools.py index 9a910df..e143b70 100644 --- a/quickff/tools.py +++ b/quickff/tools.py @@ -398,11 +398,11 @@ def get_ei_radii(numbers): 'Li': 1.2951*angstrom, 'B' : 1.2020*angstrom, 'C' : 1.1703*angstrom, 'N' : 1.1048*angstrom, 'O' : 1.1325*angstrom, 'F' : 1.1096*angstrom, 'Na': 1.7093*angstrom, 'Mg': 1.6155*angstrom, 'Al': 1.6742*angstrom, - 'Si': 1.6376*angstrom, 'P' : 1.5727*angstrom, 'S' : 1.6011*angstrom, - 'Cl': 1.5798*angstrom, 'Ca': 1.6541*angstrom, 'Sc': 2.0559*angstrom, - 'Ti': 2.0502*angstrom, 'V' : 2.0654*angstrom, 'Cr': 2.0692*angstrom, - 'Mn': 2.0323*angstrom, 'Fe': 2.0695*angstrom, 'Co': 2.0377*angstrom, - 'Ni': 2.0579*angstrom, 'Cu': 2.0573*angstrom, 'Zn': 1.9896*angstrom, + 'Si': 1.6376*angstrom, 'P' : 1.5727*angstrom, 'S' : 1.6011*angstrom, + 'Cl': 1.5798*angstrom, 'Ca': 1.6541*angstrom, 'Sc': 2.0559*angstrom, + 'Ti': 2.0502*angstrom, 'V' : 2.0654*angstrom, 'Cr': 2.0692*angstrom, + 'Mn': 2.0323*angstrom, 'Fe': 2.0695*angstrom, 'Co': 2.0377*angstrom, + 'Ni': 2.0579*angstrom, 'Cu': 2.0573*angstrom, 'Zn': 1.9896*angstrom, 'Ga': 2.0820*angstrom, 'Br': 2.0088*angstrom, } diff --git a/share/validation/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png b/share/validation/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png deleted file mode 100644 index 6820e4d..0000000 Binary files a/share/validation/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png and /dev/null differ diff --git a/share/validation/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png b/share/validation/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png deleted file mode 100644 index 30600e1..0000000 Binary files a/share/validation/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png and /dev/null differ diff --git a/share/validation/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png b/share/validation/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png deleted file mode 100644 index 0f37b16..0000000 Binary files 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