diff --git a/src/evaluator_io.py b/src/evaluator_io.py index 83c622e6b..79dbb20f4 100644 --- a/src/evaluator_io.py +++ b/src/evaluator_io.py @@ -308,10 +308,6 @@ def _parameter_value_from_gradient_key(self, gradient_key): bool Returns True if the parameter is a cosmetic one. """ - try: - import openmm.unit as simtk_unit - except ImportError: - import simtk.unit as simtk_unit parameter_handler = self.FF.openff_forcefield.get_parameter_handler( gradient_key.tag @@ -350,10 +346,7 @@ def _parameter_value_from_gradient_key(self, gradient_key): ): is_cosmetic = True - if not isinstance(parameter_value, simtk_unit.Quantity): - parameter_value = parameter_value * simtk_unit.dimensionless - - return openmm_quantity_to_pint(parameter_value), is_cosmetic + return parameter_value, is_cosmetic def _extract_physical_parameter_values(self): """Extracts an array of the values of the physical parameters diff --git a/src/smirnoffio.py b/src/smirnoffio.py index 36b444103..b5128d41f 100644 --- a/src/smirnoffio.py +++ b/src/smirnoffio.py @@ -115,7 +115,7 @@ def smirnoff_analyze_parameter_coverage(forcefield, tgt_opts): logger.info('%4i %-100s : %10d\n' % (i, p, parameter_counter[smirks])) if parameter_counter[smirks] > 0: n_covered += 1 - logger.info("SNIRNOFF Parameter Coverage Analysis result: %d/%d parameters are covered.\n" % (n_covered, len(forcefield.plist))) + logger.info("SMIRNOFF Parameter Coverage Analysis result: %d/%d parameters are covered.\n" % (n_covered, len(forcefield.plist))) logger.info("-"*118 + '\n') class SMIRNOFF_Reader(BaseReader): diff --git a/studies/022_opt_geo_target/optimize.out b/studies/022_opt_geo_target/optimize.out index 581b352b2..b173a2f99 100644 --- a/studies/022_opt_geo_target/optimize.out +++ b/studies/022_opt_geo_target/optimize.out @@ -197,7 +197,7 @@ Force field assignment data written to /home2/qyd/projects/forcebalance-dev/stud 24 vdW/Atom/rmin_half/[#6X4:1] : 2 25 vdW/Atom/epsilon/[#8X2H0+0:1] : 2 26 vdW/Atom/rmin_half/[#8X2H0+0:1] : 2 -SNIRNOFF Parameter Coverage Analysis result: 27/27 parameters are covered. +SMIRNOFF Parameter Coverage Analysis result: 27/27 parameters are covered. ---------------------------------------------------------------------------------------------------------------------- Using parabolic regularization (Gaussian prior) with strength 1.0e+00 (+), 0.0e+00 (x) #========================================================# diff --git a/studies/023_torsion_relaxed/optimize.out b/studies/023_torsion_relaxed/optimize.out index b8821010c..7339c79f0 100644 --- a/studies/023_torsion_relaxed/optimize.out +++ b/studies/023_torsion_relaxed/optimize.out @@ -1621,7 +1621,7 @@ Force field assignment data written to /home/leeping/src/forcebalance/studies/02 501 ProperTorsions/Proper/k1/[*:1]-[*:2]#[*:3]-[*:4] : 0 502 ProperTorsions/Proper/k1/[*:1]~[*:2]-[*:3]#[*:4] : 0 503 ProperTorsions/Proper/k1/[*:1]~[*:2]=[#6,#7,#16,#15;X2:3]=[*:4] : 0 -SNIRNOFF Parameter Coverage Analysis result: 19/504 parameters are covered. +SMIRNOFF Parameter Coverage Analysis result: 19/504 parameters are covered. ---------------------------------------------------------------------------------------------------------------------- Using parabolic regularization (Gaussian prior) with strength 1.0e+00 (+), 0.0e+00 (x) #========================================================# diff --git a/studies/024_openff_evaluator/output_ref/optimize.out b/studies/024_openff_evaluator/output_ref/optimize.out index 0bddcdafc..3d6fb533d 100644 --- a/studies/024_openff_evaluator/output_ref/optimize.out +++ b/studies/024_openff_evaluator/output_ref/optimize.out @@ -145,7 +145,7 @@ Force field assignment data written to XXX/smirnoff_parameter_assignments.json 7 vdW/Atom/rmin_half/[#6X4:1] : 0 8 vdW/Atom/epsilon/[#8X2H1+0:1] : 0 9 vdW/Atom/rmin_half/[#8X2H1+0:1] : 0 -SNIRNOFF Parameter Coverage Analysis result: 0/10 parameters are covered. +SMIRNOFF Parameter Coverage Analysis result: 0/10 parameters are covered. ---------------------------------------------------------------------------------------------------------------------- Using parabolic regularization (Gaussian prior) with strength 1.0e+00 (+), 0.0e+00 (x) diff --git a/studies/025_openff_recharge/output_ref/optimize.out b/studies/025_openff_recharge/output_ref/optimize.out index 50c7fe16c..c93c39f50 100644 --- a/studies/025_openff_recharge/output_ref/optimize.out +++ b/studies/025_openff_recharge/output_ref/optimize.out @@ -106,7 +106,7 @@ Force field assignment data written to /Users/boothros/PyCharmProjects/forcebala idx Parameter Count ---------------------------------------------------------------------------------------------------------------------- 0 ChargeIncrementModel/ChargeIncrement/charge_increment1/[#6X4:1]-[#1:2] : 0 -SNIRNOFF Parameter Coverage Analysis result: 0/1 parameters are covered. +SMIRNOFF Parameter Coverage Analysis result: 0/1 parameters are covered. ---------------------------------------------------------------------------------------------------------------------- Using parabolic regularization (Gaussian prior) with strength 1.0e+00 (+), 0.0e+00 (x) #========================================================# diff --git a/studies/026_smirnoff_14_scale/optimize.out b/studies/026_smirnoff_14_scale/optimize.out index 171dcb52f..74be45ca1 100644 --- a/studies/026_smirnoff_14_scale/optimize.out +++ b/studies/026_smirnoff_14_scale/optimize.out @@ -105,7 +105,7 @@ Force field assignment data written to /Users/boothros/PyCharmProjects/forcebala idx Parameter Count ---------------------------------------------------------------------------------------------------------------------- 0 /vdW/scale14 : 0 -SNIRNOFF Parameter Coverage Analysis result: 0/1 parameters are covered. +SMIRNOFF Parameter Coverage Analysis result: 0/1 parameters are covered. ---------------------------------------------------------------------------------------------------------------------- Using parabolic regularization (Gaussian prior) with strength 1.0e+00 (+), 0.0e+00 (x) #========================================================# diff --git a/studies/027_openff_hessian_target/optimize.out b/studies/027_openff_hessian_target/optimize.out index 34caa69e8..0b453a939 100644 --- a/studies/027_openff_hessian_target/optimize.out +++ b/studies/027_openff_hessian_target/optimize.out @@ -187,7 +187,7 @@ Force field assignment data written to /Users/hyesu/Project/git-repo/fb-factorie 24 vdW/Atom/epsilon/[#6X4:1] : 0 25 vdW/Atom/rmin_half/[#8X2H0+0:1] : 0 26 vdW/Atom/epsilon/[#8X2H0+0:1] : 0 -SNIRNOFF Parameter Coverage Analysis result: 6/27 parameters are covered. +SMIRNOFF Parameter Coverage Analysis result: 6/27 parameters are covered. ---------------------------------------------------------------------------------------------------------------------- Using parabolic regularization (Gaussian prior) with strength 1.0e+00 (+), 0.0e+00 (x) #========================================================#