Merge: bugfixes and improvements

ASH-packages.sh

@@ -20,6 +20,7 @@
 mamba install -c conda-forge openmm # 745MB
 #xTB: semiempirical program
 mamba install -c conda-forge xtb # 8MB
+mamba install -c conda-forge xtb-python # xtb Python API
 # pdbfixer: Needed for MM of biomolecules
 mamba install -c conda-forge pdbfixer # 0.5 MB
 #pySCF: Good QM program

README.md

@@ -10,6 +10,11 @@ ASH is a Python-based computational chemistry and QM/MM environment for molecula
 Interfaces to popular QM codes: ORCA, xTB, PySCF, MRCC, ccpy, Psi4, Dalton, CFour, TeraChem, QUICK. Interface to the OpenMM library for MM and MD algorithms. Interfaces to specialized high-level QM codes like Block, Dice and ipie for DMRG, SHCI and AFQMC calculations. Interfaces to machine-learning libraries like PyTorch, MACE and MLatom for using and training machine learning potentials.
 Excellent environment for writing simple or complex computational chemistry workflows.
 
+**Citation**
+If ASH is useful in your research please cite us:
+`ASH: a Multi-scale, Multi-theory Modeling program <https://onlinelibrary.wiley.com/doi/10.1002/jcc.70359>`_
+R. Bjornsson*,  J. Comput. Chem 2026, 47, e70359.
+
 **In case of problems:**
 Please open an issue on Github and we will try to fix any problems as soon as possible.
 

ash/__init__.py

@@ -34,14 +34,17 @@
         print("Forbidden names:", forbidden_inputfilenames)
         ashexit()
 
+# New API test
+#from . import job
+
 #Results dataclass
 from .modules.module_results import ASH_Results,read_results_from_file
 
 # Fragment class and coordinate functions
 import ash.modules.module_coords
 from .modules.module_coords import get_molecules_from_trajectory, eldict_covrad, write_pdbfile, Fragment, read_xyzfile, \
     write_xyzfile, make_cluster_from_box, read_ambercoordinates, read_gromacsfile, split_multimolxyzfile,distance_between_atoms, \
-    angle_between_atoms, dihedral_between_atoms, pdb_to_smiles, xyz_to_pdb_with_connectivity, writepdb_with_connectivity, mol_to_pdb, sdf_to_pdb
+    angle_between_atoms, dihedral_between_atoms
 from .modules.module_coords import remove_atoms_from_system_CHARMM, add_atoms_to_system_CHARMM, getwaterconstraintslist,\
     QMregionfragexpand, cut_sphere, cut_cubic_box, QMPC_fragexpand, read_xyzfiles, Reaction, define_XH_constraints, simple_get_water_constraints, print_internal_coordinate_table,\
     flexible_align_pdb, flexible_align_xyz, flexible_align, insert_solute_into_solvent, nuc_nuc_repulsion, calculate_RMSD
@@ -82,7 +85,7 @@
 from .modules.module_oniom import ONIOMTheory
 
 # Surface
-from .modules.module_surface import calc_surface, calc_surface_fromXYZ, read_surfacedict_from_file, write_surfacedict_to_file
+from .modules.module_surface_new import calc_surface, calc_surface_fromXYZ, read_surfacedict_from_file, write_surfacedict_to_file, RestraintTheory,analyze_surface
 
 # # QMcode interfaces
 from .interfaces.interface_ORCA import ORCATheory, counterpoise_calculation_ORCA, ORCA_External_Optimizer, run_orca_plot, MolecularOrbitalGrab, \
@@ -113,7 +116,7 @@
 from .interfaces.interface_MNDO import MNDOTheory
 
 from .interfaces.interface_CFour import CFourTheory, run_CFour_HLC_correction, run_CFour_DBOC_correction, convert_CFour_Molden_file
-from .interfaces.interface_xtb import xTBTheory, gxTBTheory
+from .interfaces.interface_xtb import xTBTheory, gxTBTheory,tbliteTheory
 from .interfaces.interface_DFTB import DFTBTheory
 from .interfaces.interface_PyMBE import PyMBETheory
 from .interfaces.interface_MLatom import MLatomTheory
@@ -123,6 +126,8 @@
 from .interfaces.interface_mace import MACETheory
 from .interfaces.interface_fairchem import FairchemTheory
 from .interfaces.interface_packmol import packmol_solvate
+from .interfaces.interface_openbabel import OpenBabelTheory, pdb_to_smiles, mol_to_pdb, sdf_to_pdb, writepdb_with_connectivity, \
+                                            xyz_to_pdb_with_connectivity
 
 # MM: external and internal
 from .interfaces.interface_OpenMM import OpenMMTheory, OpenMM_MD, OpenMM_MDclass, OpenMM_Opt, OpenMM_Modeller, \
@@ -150,9 +155,12 @@
 from .modules.module_QMMM import QMMMTheory, actregiondefine, read_charges_from_psf, compute_decomposed_QM_MM_energy
 from .modules.module_polembed import PolEmbedTheory
 
-# Knarr
+# Knarric_optimizer_alte
 from .interfaces.interface_knarr import NEB, NEBTS, interpolation_geodesic
 
+# FSM
+from .interfaces.interface_fsm import FSM
+
 #VMD
 from .interfaces.interface_VMD import write_VMD_script_cube
 
@@ -171,8 +179,7 @@
 from .modules.module_molcrys import molcrys, Fragmenttype
 
 # Geometry optimization
-from .functions.functions_optimization import SimpleOpt, BernyOpt
-from .interfaces.interface_dlfind import DLFIND_optimizer
+from .functions.functions_optimization import SimpleOpt, BernyOpt, periodic_optimizer_alternating, Cart_optimizer, Cart_optimizer_class
 
 # geomeTRIC interface
 from .interfaces.interface_geometric_new import geomeTRICOptimizer,GeomeTRICOptimizerClass
@@ -205,7 +212,13 @@
 
 # Plotting
 import ash.modules.module_plotting
-from .modules.module_plotting import reactionprofile_plot, contourplot, plot_Spectrum, MOplot_vertical, ASH_plot
+from .modules.module_plotting import reactionprofile_plot, contourplot, volumeplot, plot_Spectrum, MOplot_vertical, ASH_plot
+
+# DL-FIND
+from ash.interfaces.interface_dlfind import DLFIND_optimizer,DLFIND_optimizerClass
+
+# Sella
+from ash.interfaces.interface_sella import SellaOptimizer, SellaoptimizerClass
 
 # Other
 import ash.interfaces.interface_crest
@@ -240,3 +253,5 @@
         ash.settings_ash.settings_dict["connectivity_code"] = "py"
         # LJ+Coulomb and pairpot arrays in nonbonded MM
         ash.settings_ash.settings_dict["nonbondedMM_code"] = "py"
+
+

ash/databases/fragments/3fgaba.xyz

@@ -0,0 +1,18 @@
+16
+0 1
+O          -2.94954451337551    0.41756772104132    0.39570906486802
+C          -1.94726532077404    0.00496590632354   -0.21387039282475
+O          -1.86486267613291   -0.98425618175571   -0.96529807180037
+C          -0.63082938495411    0.85257294318251   -0.03309484428487
+C           0.59645164744937   -0.03287653921399   -0.06815433659886
+C           1.90438518068492    0.74037017428706   -0.24605311458592
+N           3.05907283524481   -0.19683120033081   -0.20769489026400
+H          -0.60859388824722    1.55863625302213   -0.86234378437503
+H          -0.70691653721786    1.39879504806108    0.90589734163572
+F           0.71886137831986   -0.72287937449757    1.14252449306844
+H           0.44625382173731   -0.80706377016452   -0.83173237571128
+H           1.87791981471676    1.27078699161807   -1.19694917851462
+H           1.99775942946239    1.45578778965541    0.57362920347930
+H           3.95147619228729    0.31823090034354   -0.21891777872034
+H           3.02685050790199   -0.84412002131880   -1.00946488836316
+H           2.99602715486291   -0.75495857538077    0.65883171551972

ash/functions/functions_elstructure.py

@@ -10,7 +10,7 @@
 import ash.constants
 import ash.modules.module_coords
 import ash.dictionaries_lists
-from ash.functions.functions_general import ashexit, isodd, print_line_with_mainheader,pygrep,print_pretty_table
+from ash.functions.functions_general import ashexit, check_program_location, isodd, print_line_with_mainheader,pygrep,print_pretty_table
 from ash.interfaces.interface_ORCA import ORCATheory, run_orca_plot, make_molden_file_ORCA
 from ash.modules.module_coords import nucchargelist,elematomnumbers
 from ash.dictionaries_lists import eldict
@@ -669,16 +669,15 @@ def DDEC_calc(elems=None, theory=None, gbwfile=None, numcores=1, DDECmodel='DDEC
     else:
         print("Found molden2aim.exe: ", molden2aim)
 
-    print("Warning: DDEC_calc requires chargemol-binary dir to be present in environment PATH variable.")
+    print("Warning: DDEC_calc requires chargemol binary in PATH")
 
     #Finding chargemoldir from PATH in os.path
     PATH=os.environ.get('PATH').split(':')
     print("PATH: ", PATH)
     print("Searching for molden2aim and chargemol in PATH")
-    for p in PATH:
-        if 'chargemol' in p:
-            print("Found chargemol in path line (this dir should contain the executables):", p)
-            chargemolbinarydir=p
+
+
+    chargemolbinarydir = check_program_location(None,None, "chargemol")
 
     #Checking if we can proceed
     if chargemolbinarydir is None:
@@ -1820,6 +1819,12 @@ def create_cubefile_from_orbfile(orbfile, option='density', grid=3, delete_temp_
         mfile = make_molden_file_ORCA(orbfile, printlevel=printlevel)
     print("Now using Multiwfn to create cube file from Moldenfile")
     cubefile = multiwfn_run(mfile, option=option, grid=grid, printlevel=printlevel)
+    if cubefile is None and option == 'spin-density' or option == 'spindensity':
+        if os.path.exists('spindensity.cub'):
+            cubefile = 'spindensity.cub'
+        else:
+            print("Spin density cube file not found. Something went wrong.")
+            ashexit()
     # Rename cubefile (shortens it)
     new_cubename=str(os.path.splitext(orbfile)[0])+".cube"
     os.rename(cubefile, new_cubename)
@@ -2595,3 +2600,14 @@ def density_sensitivity_metric(fragment=None, functional="B3LYP", basis="def2-TZ
     #TODO: Option to plot difference density also
 
     return metrics_dict
+
+def boltzmann_populations(energies, temperature=298.15):
+    print("Inside boltzmann_populations function")
+    beta = 1/(ash.constants.R_gasconst_kcalK*temperature)
+
+    rel_energies=np.array([en-min(energies) for en in energies])*ash.constants.hartokcal
+    print("Relative energies (kcal/mol):", rel_energies)
+    boltzmann_factors = np.exp(-1*rel_energies * beta)
+    populations = boltzmann_factors / np.sum(boltzmann_factors)
+    print("Boltzmann populations at", temperature, "K:", populations)
+    return populations

ash/functions/functions_molcrys.py

@@ -243,7 +243,7 @@ def same_fragment(fragtype=None, nuccharge=None, mass=None, formula=None):
         printdebug("el_list:", el_list)
         printdebug("current_mass:", current_mass)
         formula = ash.modules.module_coords.elemlisttoformula(el_list)
-        print("formula:", formula)
+        #print("formula:", formula)
         for fragment in fragments:
             printdebug("el_list:", el_list)
             ncharge = ash.modules.module_coords.nucchargelist(el_list)