diff --git a/package/ClayCode/core/classes.py b/package/ClayCode/core/classes.py index 8ea76da9..ee57aa5f 100644 --- a/package/ClayCode/core/classes.py +++ b/package/ClayCode/core/classes.py @@ -2007,6 +2007,13 @@ def __init__(self, path: Union[BasicPath, Dir], check=False, order=None): # self._data.append(FileFactory(file, check=check)) self.data = self._data + def __repr__(self): + return ( + f"{self.__class__.__name__}({self.path.name}: " + + ", ".join([file.name for file in self.data]) + + ")" + ) + class PathList(FileList): pass diff --git a/package/ClayCode/core/consts.py b/package/ClayCode/core/consts.py index 5994eab4..6738b958 100644 --- a/package/ClayCode/core/consts.py +++ b/package/ClayCode/core/consts.py @@ -39,3 +39,5 @@ TABSIZE = 4 ANGSTROM = "\u212B" +GREATER_EQUAL = "\u2265" +LESS_EQUAL = "\u2264" diff --git a/package/ClayCode/core/lib.py b/package/ClayCode/core/lib.py index f39af835..3a0eca6c 100644 --- a/package/ClayCode/core/lib.py +++ b/package/ClayCode/core/lib.py @@ -167,6 +167,7 @@ def run_analysis(instance: analysis_class, start: int, stop: int, step: int): if v is not None: kwarg_dict[k] = v instance.run(**kwarg_dict) + return instance @overload @@ -217,37 +218,53 @@ def get_selections(infiles, sel, clay_type, other=None, in_memory=False): u = MDAnalysis.Universe(*infiles, in_memory=in_memory) # only resname specified if len(sel) == 1: + sel_str = sel[0] sel = u.select_atoms(f"resname {sel[0]}") + # rename and atom type specified elif len(sel) == 2: # expand search string for terminal O atom types if sel[1] == "OT*": sel[1] = "OT* O OXT" + sel_str = "{}: {}".format(*sel) sel = u.select_atoms(f"resname {sel[0]}* and name {sel[1]}") + else: raise ValueError('Expected 1 or 2 arguments for "sel"') + if other is None: pass elif len(other) == 1: logger.debug(f"other: {other}") + other_str = other[0] other = u.select_atoms(f"resname {other[0]}") + elif len(other) == 2: logger.debug(f"other: {other}") if other[1] == "OT*": other[1] = "OT* O OXT" + other_str = "{}: {}".format(*other) other = u.select_atoms(f"resname {other[0]}* and name {other[1]}") else: raise ValueError('Expected 1 or 2 arguments for "other"') clay = u.select_atoms(f"resname {clay_type}* and name OB* o*") - logger.finfo( - f"'clay': Selected {clay.n_atoms} atoms of " - f"{clay.n_residues} {clay_type!r} unit cells" + # logger.finfo( + # f"'clay': Selected {clay.n_atoms} atoms of " + # f"{clay.n_residues} unit cells" + # ) + log_atomgroup_info( + ag=clay, ag_name=clay_type, kwd_str="Clay unit cell type" ) sel = select_outside_clay_stack(sel, clay) # Clay + two other atom groups selected + log_atomgroup_info(ag=sel, ag_name=sel_str, kwd_str="Atom selection") + if other is not None: other = select_outside_clay_stack(other, clay) + log_atomgroup_info( + ag=other, ag_name=other_str, kwd_str="Second atom selection" + ) return sel, clay, other # Only clay + one other atom group selected @@ -255,6 +272,23 @@ def get_selections(infiles, sel, clay_type, other=None, in_memory=False): return sel, clay +def get_ag_numbers_info(ag: AtomGroup) -> Tuple[int, int]: + return "Selected {} atoms in {} residues.".format( + ag.n_atoms, ag.n_residues + ) + + +def log_atomgroup_info(ag: AtomGroup, kwd_str: str, ag_name: str): + if ag.n_atoms > 0: + logger.finfo(f"{ag_name!r}", kwd_str=f"{kwd_str}: ") + logger.finfo(get_ag_numbers_info(ag)) + else: + logger.error( + f"{ag_name} contains 0 atoms. Check atom selection parameters." + ) + sys.exit(1) + + def select_clay( universe: MDAnalysis.Universe, ff: Optional[ForceField] = None, @@ -568,7 +602,7 @@ def select_cyzone( :rtype: NoReturn """ z_col = distances[:, :, 2] - z_col.mask = np.abs(distances[:, :, 2]) > z_dist + z_col.mask = np.abs(z_col) > z_dist distances.mask = np.broadcast_to( z_col.mask[:, :, np.newaxis], distances.shape ) diff --git a/package/ClayCode/core/parsing.py b/package/ClayCode/core/parsing.py index 9739a18e..541ee8ca 100644 --- a/package/ClayCode/core/parsing.py +++ b/package/ClayCode/core/parsing.py @@ -275,6 +275,127 @@ "analyse", help="Analyse clay simulations." ) +analysisparser.add_argument( + "-name", type=str, help="System name", dest="sysname", required=True +) +analysisparser.add_argument( + "-inp", + type=str, + help="Input file names", + nargs=2, + metavar=("coordinates", "trajectory"), + dest="infiles", + required=False, +) +analysisparser.add_argument( + "-inpname", + type=str, + help="Input file names", + metavar="name_stem", + dest="inpname", + required=False, +) +analysisparser.add_argument( + "-uc", + type=str, + help="Clay unit cell type", + dest="clay_type", + required=True, +) +analysisparser.add_argument( + "-sel", + type=str, + nargs="+", + help="Atom type selection", + dest="sel", + required=True, +) +analysisparser.add_argument( + "-n_bins", + default=None, + type=int, + help="Number of bins in histogram", + dest="n_bins", +) +analysisparser.add_argument( + "-bin_step", + type=float, + default=None, + help="bin size in histogram", + dest="bin_step", +) +analysisparser.add_argument( + "-xyrad", + type=float, + default=3, + help="xy-radius for calculating z-position clay surface", + dest="xyrad", +) +analysisparser.add_argument( + "-cutoff", + type=float, + default=20, + help="cutoff in z-direction", + dest="cutoff", +) + +analysisparser.add_argument( + "-start", + type=int, + default=None, + help="First frame for analysis.", + dest="start", +) +analysisparser.add_argument( + "-step", + type=int, + default=None, + help="Frame steps for analysis.", + dest="step", +) +analysisparser.add_argument( + "-stop", + type=int, + default=None, + help="Last frame for analysis.", + dest="stop", +) +analysisparser.add_argument( + "-out", + type=str, + help="Filename for results pickle.", + dest="save", + default=True, +) +analysisparser.add_argument( + "-check_traj", + type=int, + default=False, + help="Expected trajectory length.", + dest="check_traj_len", +) +analysisparser.add_argument( + "--write_z", + type=str, + default=True, + help="Binary array output of selection z-distances.", + dest="write", +) +analysisparser.add_argument( + "--overwrite", + action="store_true", + default=False, + help="Overwrite existing z-distance array data.", + dest="overwrite", +) +analysisparser.add_argument( + "--update", + action="store_true", + default=False, + help="Overwrite existing trajectory and coordinate array data.", + dest="new", +) + # plot analysis results plotparser = subparsers.add_parser( "plot", help="Plot simulation analysis results" @@ -309,6 +430,7 @@ dest="yaml_file", ) + # siminp_subparsers = siminpparser.add_subparsers() # dspace_arg_group = siminpparser.add_argument_group("il_spacing") @@ -703,7 +825,9 @@ def check(self) -> None: ) if tbc_match: pass - self.uc_stem = self._uc_path.itp_filelist[0].stem[:-3] + self.uc_stem = self._uc_path.itp_filelist.filter( + "[A-Z][A-Z0-9]\d\d\d" + )[0].stem[:-3] logger.debug(f"Setting unit cell type: {self._uc_name!r}") else: raise ValueError(f"Unknown unit cell type {uc_type!r}!") diff --git a/package/ClayCode/data/data/UCS/D21/D2000.gro b/package/ClayCode/data/data/UCS/D21/D2000.gro new file mode 100644 index 00000000..9d3c8bc7 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2000.gro @@ -0,0 +1,43 @@ +trans-vacant dioctahedral smectite, Garfield Nontronite, AMCSD: 0007180 +40 + 1D200 HO1 1 0.183 0.000 0.583 + 1D200 HO2 2 0.447 0.457 0.583 + 1D200 HO3 3 0.158 0.000 0.377 + 1D200 HO4 4 0.422 0.457 0.377 + 1D200 OH1 5 0.084 0.000 0.583 + 1D200 OH2 6 0.348 0.457 0.583 + 1D200 OH3 7 0.257 0.000 0.377 + 1D200 OH4 8 -0.007 0.457 0.377 + 1D200 OB1 9 0.049 0.285 0.590 + 1D200 OB2 10 0.312 0.742 0.590 + 1D200 OB3 11 0.049 0.629 0.590 + 1D200 OB4 12 0.312 0.172 0.590 + 1D200 OB5 13 0.292 0.285 0.370 + 1D200 OB6 14 0.029 0.742 0.370 + 1D200 OB7 15 0.292 0.629 0.370 + 1D200 OB8 16 0.029 0.172 0.370 + 1D200 OB9 17 0.009 0.457 0.796 + 1D200 OB10 18 0.272 0.000 0.796 + 1D200 OB11 19 0.333 0.457 0.164 + 1D200 OB12 20 0.069 0.000 0.164 + 1D200 OB13 21 0.401 0.686 0.814 + 1D200 OB14 22 0.137 0.229 0.814 + 1D200 OB15 23 0.401 0.229 0.814 + 1D200 OB16 24 0.137 0.686 0.814 + 1D200 OB17 25 0.468 0.686 0.146 + 1D200 OB18 26 0.204 0.229 0.146 + 1D200 OB19 27 0.468 0.229 0.146 + 1D200 OB20 28 0.204 0.686 0.146 + 1D200 FEO1 29 0.171 0.152 0.480 + 1D200 FEO2 30 0.434 0.609 0.480 + 1D200 FEO3 31 0.171 0.762 0.480 + 1D200 FEO4 32 0.434 0.305 0.480 + 1D200 ST1 33 0.017 0.301 0.753 + 1D200 ST2 34 0.281 0.758 0.753 + 1D200 ST3 35 0.017 0.613 0.753 + 1D200 ST4 36 0.281 0.156 0.753 + 1D200 ST5 37 0.324 0.301 0.207 + 1D200 ST6 38 0.060 0.758 0.207 + 1D200 ST7 39 0.324 0.613 0.207 + 1D200 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 diff --git a/package/ClayCode/data/data/UCS/D21/D2000.itp b/package/ClayCode/data/data/UCS/D21/D2000.itp new file mode 100644 index 00000000..9bd6ad03 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2000.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2000 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2000rtp D2000q 0.0 + 1 ho 1 D2000 HO1 1 0.425 1.008 + 2 ho 1 D2000 HO2 2 0.425 1.008 + 3 ho 1 D2000 HO3 3 0.425 1.008 + 4 ho 1 D2000 HO4 4 0.425 1.008 + 5 oh 1 D2000 OH1 5 -0.95 16 + 6 oh 1 D2000 OH2 6 -0.95 16 + 7 oh 1 D2000 OH3 7 -0.95 16 + 8 oh 1 D2000 OH4 8 -0.95 16 + 9 ob 1 D2000 OB1 9 -1.05 16 + 10 ob 1 D2000 OB2 10 -1.05 16 + 11 ob 1 D2000 OB3 11 -1.05 16 + 12 ob 1 D2000 OB4 12 -1.05 16 + 13 ob 1 D2000 OB5 13 -1.05 16 + 14 ob 1 D2000 OB6 14 -1.05 16 + 15 ob 1 D2000 OB7 15 -1.05 16 + 16 ob 1 D2000 OB8 16 -1.05 16 + 17 ob 1 D2000 OB9 17 -1.05 16 + 18 ob 1 D2000 OB10 18 -1.05 16 + 19 ob 1 D2000 OB11 19 -1.05 16 + 20 ob 1 D2000 OB12 20 -1.05 16 + 21 ob 1 D2000 OB13 21 -1.05 16 + 22 ob 1 D2000 OB14 22 -1.05 16 + 23 ob 1 D2000 OB15 23 -1.05 16 + 24 ob 1 D2000 OB16 24 -1.05 16 + 25 ob 1 D2000 OB17 25 -1.05 16 + 26 ob 1 D2000 OB18 26 -1.05 16 + 27 ob 1 D2000 OB19 27 -1.05 16 + 28 ob 1 D2000 OB20 28 -1.05 16 + 29 feo 1 D2000 FEO1 29 1.575 55.845 + 30 feo 1 D2000 FEO2 30 1.575 55.845 + 31 feo 1 D2000 FEO3 31 1.575 55.845 + 32 feo 1 D2000 FEO4 32 1.575 55.845 + 33 st 1 D2000 ST1 33 2.1 28.09 + 34 st 1 D2000 ST2 34 2.1 28.09 + 35 st 1 D2000 ST3 35 2.1 28.09 + 36 st 1 D2000 ST4 36 2.1 28.09 + 37 st 1 D2000 ST5 37 2.1 28.09 + 38 st 1 D2000 ST6 38 2.1 28.09 + 39 st 1 D2000 ST7 39 2.1 28.09 + 40 st 1 D2000 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2001.gro b/package/ClayCode/data/data/UCS/D21/D2001.gro new file mode 100644 index 00000000..019ff9e3 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2001.gro @@ -0,0 +1,43 @@ +Nontronite Unit Cell 1 +40 + 1D201 HO1 1 0.183 0.000 0.583 + 1D201 HO2 2 0.447 0.457 0.583 + 1D201 HO3 3 0.158 0.000 0.377 + 1D201 HO4 4 0.422 0.457 0.377 + 1D201 OH1 5 0.084 0.000 0.583 + 1D201 OH2 6 0.348 0.457 0.583 + 1D201 OH3 7 0.257 0.000 0.377 + 1D201 OH4 8 -0.007 0.457 0.377 + 1D201 OB1 9 0.049 0.285 0.590 + 1D201 OB2 10 0.312 0.742 0.590 + 1D201 OB3 11 0.049 0.629 0.590 + 1D201 OB4 12 0.312 0.172 0.590 + 1D201 OB5 13 0.292 0.285 0.370 + 1D201 OB6 14 0.029 0.742 0.370 + 1D201 OB7 15 0.292 0.629 0.370 + 1D201 OB8 16 0.029 0.172 0.370 + 1D201 OB9 17 0.009 0.457 0.796 + 1D201 OB10 18 0.272 0.000 0.796 + 1D201 OB11 19 0.333 0.457 0.164 + 1D201 OB12 20 0.069 0.000 0.164 + 1D201 OB13 21 0.401 0.686 0.814 + 1D201 OB14 22 0.137 0.229 0.814 + 1D201 OB15 23 0.401 0.229 0.814 + 1D201 OB16 24 0.137 0.686 0.814 + 1D201 OB17 25 0.468 0.686 0.146 + 1D201 OB18 26 0.204 0.229 0.146 + 1D201 OB19 27 0.468 0.229 0.146 + 1D201 OB20 28 0.204 0.686 0.146 + 1D201 FEO1 29 0.171 0.152 0.480 + 1D201 FEO2 30 0.434 0.609 0.480 + 1D201 FEO3 31 0.171 0.762 0.480 + 1D201 FEO4 32 0.434 0.305 0.480 + 1D201 ST1 33 0.017 0.301 0.753 + 1D201 ST2 34 0.281 0.758 0.753 + 1D201 ST3 35 0.017 0.613 0.753 + 1D201 ST4 36 0.281 0.156 0.753 + 1D201 ST5 37 0.324 0.301 0.207 + 1D201 ST6 38 0.060 0.758 0.207 + 1D201 ST7 39 0.324 0.613 0.207 + 1D201 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 diff --git a/package/ClayCode/data/data/UCS/D21/D2001.itp b/package/ClayCode/data/data/UCS/D21/D2001.itp new file mode 100644 index 00000000..b55b0078 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2001.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2001 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2001rtp D2001q 0.0 + 1 ho 1 D2001 HO1 1 0.425 1.008 + 2 ho 1 D2001 HO2 2 0.425 1.008 + 3 ho 1 D2001 HO3 3 0.425 1.008 + 4 ho 1 D2001 HO4 4 0.425 1.008 + 5 oh 1 D2001 OH1 5 -0.95 16 + 6 oh 1 D2001 OH2 6 -0.95 16 + 7 oh 1 D2001 OH3 7 -0.95 16 + 8 oh 1 D2001 OH4 8 -0.95 16 + 9 ob 1 D2001 OB1 9 -1.05 16 + 10 ob 1 D2001 OB2 10 -1.05 16 + 11 ob 1 D2001 OB3 11 -1.05 16 + 12 ob 1 D2001 OB4 12 -1.05 16 + 13 ob 1 D2001 OB5 13 -1.05 16 + 14 ob 1 D2001 OB6 14 -1.05 16 + 15 ob 1 D2001 OB7 15 -1.05 16 + 16 ob 1 D2001 OB8 16 -1.05 16 + 17 ob 1 D2001 OB9 17 -1.05 16 + 18 ob 1 D2001 OB10 18 -1.05 16 + 19 ob 1 D2001 OB11 19 -1.05 16 + 20 ob 1 D2001 OB12 20 -1.05 16 + 21 ob 1 D2001 OB13 21 -1.05 16 + 22 ob 1 D2001 OB14 22 -1.05 16 + 23 ob 1 D2001 OB15 23 -1.05 16 + 24 ob 1 D2001 OB16 24 -1.05 16 + 25 ob 1 D2001 OB17 25 -1.05 16 + 26 ob 1 D2001 OB18 26 -1.05 16 + 27 ob 1 D2001 OB19 27 -1.05 16 + 28 ob 1 D2001 OB20 28 -1.05 16 + 29 feo 1 D2001 FEO1 29 1.575 55.845 + 30 feo 1 D2001 FEO2 30 1.575 55.845 + 31 feo 1 D2001 FEO3 31 1.575 55.845 + 32 feo 1 D2001 FEO4 32 1.575 55.845 + 33 st 1 D2001 ST1 33 2.1 28.09 + 34 st 1 D2001 ST2 34 2.1 28.09 + 35 st 1 D2001 ST3 35 2.1 28.09 + 36 st 1 D2001 ST4 36 2.1 28.09 + 37 st 1 D2001 ST5 37 2.1 28.09 + 38 st 1 D2001 ST6 38 2.1 28.09 + 39 st 1 D2001 ST7 39 2.1 28.09 + 40 st 1 D2001 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2002.gro b/package/ClayCode/data/data/UCS/D21/D2002.gro new file mode 100644 index 00000000..0228ce3f --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2002.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 2 +40 + 1D202 HO1 1 0.183 0.000 0.583 + 1D202 HO2 2 0.447 0.457 0.583 + 1D202 HO3 3 0.158 0.000 0.377 + 1D202 HO4 4 0.422 0.457 0.377 + 1D202 OH1 5 0.084 0.000 0.583 + 1D202 OH2 6 0.348 0.457 0.583 + 1D202 OH3 7 0.257 0.000 0.377 + 1D202 OH4 8 -0.007 0.457 0.377 + 1D202 OBTS1 9 0.049 0.285 0.590 + 1D202 OB2 10 0.312 0.742 0.590 + 1D202 OB3 11 0.049 0.629 0.590 + 1D202 OB4 12 0.312 0.172 0.590 + 1D202 OB5 13 0.292 0.285 0.370 + 1D202 OB6 14 0.029 0.742 0.370 + 1D202 OB7 15 0.292 0.629 0.370 + 1D202 OB8 16 0.029 0.172 0.370 + 1D202 OBTS9 17 0.009 0.457 0.796 + 1D202 OB10 18 0.272 0.000 0.796 + 1D202 OB11 19 0.333 0.457 0.164 + 1D202 OB12 20 0.069 0.000 0.164 + 1D202 OB13 21 0.401 0.686 0.814 + 1D202 OBT14 22 0.137 0.229 0.814 + 1D202 OBT15 23 0.401 0.229 0.814 + 1D202 OB16 24 0.137 0.686 0.814 + 1D202 OB17 25 0.468 0.686 0.146 + 1D202 OB18 26 0.204 0.229 0.146 + 1D202 OB19 27 0.468 0.229 0.146 + 1D202 OB20 28 0.204 0.686 0.146 + 1D202 FEO1 29 0.171 0.152 0.480 + 1D202 AO2 30 0.434 0.609 0.480 + 1D202 FEO3 31 0.171 0.762 0.480 + 1D202 FEO4 32 0.434 0.305 0.480 + 1D202 AT1 33 0.017 0.301 0.753 + 1D202 ST2 34 0.281 0.758 0.753 + 1D202 ST3 35 0.017 0.613 0.753 + 1D202 ST4 36 0.281 0.156 0.753 + 1D202 ST5 37 0.324 0.301 0.207 + 1D202 ST6 38 0.060 0.758 0.207 + 1D202 ST7 39 0.324 0.613 0.207 + 1D202 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2002.itp b/package/ClayCode/data/data/UCS/D21/D2002.itp new file mode 100644 index 00000000..4cf50e00 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2002.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2002 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2002rtp D2002q -1.0 + 1 ho 1 D2002 HO1 1 0.425 1.008 + 2 ho 1 D2002 HO2 2 0.425 1.008 + 3 ho 1 D2002 HO3 3 0.425 1.008 + 4 ho 1 D2002 HO4 4 0.425 1.008 + 5 oh 1 D2002 OH1 5 -0.95 16 + 6 oh 1 D2002 OH2 6 -0.95 16 + 7 oh 1 D2002 OH3 7 -0.95 16 + 8 oh 1 D2002 OH4 8 -0.95 16 + 9 obts 1 D2002 OBTS1 9 -1.16875 16 ; OB on Td Al + 10 ob 1 D2002 OB2 10 -1.05 16 + 11 ob 1 D2002 OB3 11 -1.05 16 + 12 ob 1 D2002 OB4 12 -1.05 16 + 13 ob 1 D2002 OB5 13 -1.05 16 + 14 ob 1 D2002 OB6 14 -1.05 16 + 15 ob 1 D2002 OB7 15 -1.05 16 + 16 ob 1 D2002 OB8 16 -1.05 16 + 17 obts 1 D2002 OBTS9 17 -1.16875 16 ; OB on Td Al + 18 ob 1 D2002 OB10 18 -1.05 16 + 19 ob 1 D2002 OB11 19 -1.05 16 + 20 ob 1 D2002 OB12 20 -1.05 16 + 21 ob 1 D2002 OB13 21 -1.05 16 + 22 obts 1 D2002 OBT14 22 -1.16875 16 ; OB on Td Al + 23 obts 1 D2002 OBT15 23 -1.16875 16 ; OB on Td Al + 24 ob 1 D2002 OB16 24 -1.05 16 + 25 ob 1 D2002 OB17 25 -1.05 16 + 26 ob 1 D2002 OB18 26 -1.05 16 + 27 ob 1 D2002 OB19 27 -1.05 16 + 28 ob 1 D2002 OB20 28 -1.05 16 + 29 feo 1 D2002 FEO1 29 1.575 55.845 + 30 ao 1 D2002 AO2 30 1.575 26.98 ; subs Oct Al + 31 feo 1 D2002 FEO3 31 1.575 55.845 + 32 feo 1 D2002 FEO4 32 1.575 55.845 + 33 at 1 D2002 AT1 33 1.575 26.98 ; subs Td Al + 34 st 1 D2002 ST2 34 2.1 28.09 + 35 st 1 D2002 ST3 35 2.1 28.09 + 36 st 1 D2002 ST4 36 2.1 28.09 + 37 st 1 D2002 ST5 37 2.1 28.09 + 38 st 1 D2002 ST6 38 2.1 28.09 + 39 st 1 D2002 ST7 39 2.1 28.09 + 40 st 1 D2002 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2003.gro b/package/ClayCode/data/data/UCS/D21/D2003.gro new file mode 100644 index 00000000..5e8d6b44 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2003.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 3 +40 + 1D203 HO1 1 0.183 0.000 0.583 + 1D203 HO2 2 0.447 0.457 0.583 + 1D203 HO3 3 0.158 0.000 0.377 + 1D203 HO4 4 0.422 0.457 0.377 + 1D203 OH1 5 0.084 0.000 0.583 + 1D203 OH2 6 0.348 0.457 0.583 + 1D203 OH3 7 0.257 0.000 0.377 + 1D203 OH4 8 -0.007 0.457 0.377 + 1D203 OB1 9 0.049 0.285 0.590 + 1D203 OB2 10 0.312 0.742 0.590 + 1D203 OB3 11 0.049 0.629 0.590 + 1D203 OB4 12 0.312 0.172 0.590 + 1D203 OBTS5 13 0.292 0.285 0.370 + 1D203 OB6 14 0.029 0.742 0.370 + 1D203 OB7 15 0.292 0.629 0.370 + 1D203 OB8 16 0.029 0.172 0.370 + 1D203 OB9 17 0.009 0.457 0.796 + 1D203 OB10 18 0.272 0.000 0.796 + 1D203 OBT11 19 0.333 0.457 0.164 + 1D203 OB12 20 0.069 0.000 0.164 + 1D203 OB13 21 0.401 0.686 0.814 + 1D203 OB14 22 0.137 0.229 0.814 + 1D203 OB15 23 0.401 0.229 0.814 + 1D203 OB16 24 0.137 0.686 0.814 + 1D203 OB17 25 0.468 0.686 0.146 + 1D203 OBT18 26 0.204 0.229 0.146 + 1D203 OBT19 27 0.468 0.229 0.146 + 1D203 OB20 28 0.204 0.686 0.146 + 1D203 FEO1 29 0.171 0.152 0.480 + 1D203 FEO2 30 0.434 0.609 0.480 + 1D203 AO3 31 0.171 0.762 0.480 + 1D203 FEO4 32 0.434 0.305 0.480 + 1D203 ST1 33 0.017 0.301 0.753 + 1D203 ST2 34 0.281 0.758 0.753 + 1D203 ST3 35 0.017 0.613 0.753 + 1D203 ST4 36 0.281 0.156 0.753 + 1D203 AT5 37 0.324 0.301 0.207 + 1D203 ST6 38 0.060 0.758 0.207 + 1D203 ST7 39 0.324 0.613 0.207 + 1D203 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2003.itp b/package/ClayCode/data/data/UCS/D21/D2003.itp new file mode 100644 index 00000000..5be0bbdc --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2003.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2003 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2003rtp D2003q -1.0 + 1 ho 1 D2003 HO1 1 0.425 1.008 + 2 ho 1 D2003 HO2 2 0.425 1.008 + 3 ho 1 D2003 HO3 3 0.425 1.008 + 4 ho 1 D2003 HO4 4 0.425 1.008 + 5 oh 1 D2003 OH1 5 -0.95 16 + 6 oh 1 D2003 OH2 6 -0.95 16 + 7 oh 1 D2003 OH3 7 -0.95 16 + 8 oh 1 D2003 OH4 8 -0.95 16 + 9 ob 1 D2003 OB1 9 -1.05 16 + 10 ob 1 D2003 OB2 10 -1.05 16 + 11 ob 1 D2003 OB3 11 -1.05 16 + 12 ob 1 D2003 OB4 12 -1.05 16 + 13 obts 1 D2003 OBTS5 13 -1.16875 16 ; OB on Td Al + 14 ob 1 D2003 OB6 14 -1.05 16 + 15 ob 1 D2003 OB7 15 -1.05 16 + 16 ob 1 D2003 OB8 16 -1.05 16 + 17 ob 1 D2003 OB9 17 -1.05 16 + 18 ob 1 D2003 OB10 18 -1.05 16 + 19 obts 1 D2003 OBT11 19 -1.16875 16 ; OB on Td Al + 20 ob 1 D2003 OB12 20 -1.05 16 + 21 ob 1 D2003 OB13 21 -1.05 16 + 22 ob 1 D2003 OB14 22 -1.05 16 + 23 ob 1 D2003 OB15 23 -1.05 16 + 24 ob 1 D2003 OB16 24 -1.05 16 + 25 ob 1 D2003 OB17 25 -1.05 16 + 26 obts 1 D2003 OBT18 26 -1.16875 16 ; OB on Td Al + 27 obts 1 D2003 OBT19 27 -1.16875 16 ; OB on Td Al + 28 ob 1 D2003 OB20 28 -1.05 16 + 29 feo 1 D2003 FEO1 29 1.575 55.845 + 30 feo 1 D2003 FEO2 30 1.575 55.845 + 31 ao 1 D2003 AO3 31 1.575 26.98 ; subs Oct Al + 32 feo 1 D2003 FEO4 32 1.575 55.845 + 33 st 1 D2003 ST1 33 2.1 26.98 + 34 st 1 D2003 ST2 34 2.1 28.09 + 35 st 1 D2003 ST3 35 2.1 28.09 + 36 st 1 D2003 ST4 36 2.1 28.09 + 37 at 1 D2003 AT5 37 1.575 26.98 ; subs Td Al + 38 st 1 D2003 ST6 38 2.1 28.09 + 39 st 1 D2003 ST7 39 2.1 28.09 + 40 st 1 D2003 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2004.gro b/package/ClayCode/data/data/UCS/D21/D2004.gro new file mode 100644 index 00000000..3c46d824 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2004.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 4 +40 + 1D204 HO1 1 0.183 0.000 0.583 + 1D204 HO2 2 0.447 0.457 0.583 + 1D204 HO3 3 0.158 0.000 0.377 + 1D204 HO4 4 0.422 0.457 0.377 + 1D204 OH1 5 0.084 0.000 0.583 + 1D204 OHS2 6 0.348 0.457 0.583 + 1D204 OH3 7 0.257 0.000 0.377 + 1D204 OHS4 8 -0.007 0.457 0.377 + 1D204 OBOS1 9 0.049 0.285 0.590 + 1D204 OB2 10 0.312 0.742 0.590 + 1D204 OB3 11 0.049 0.629 0.590 + 1D204 OBOS4 12 0.312 0.172 0.590 + 1D204 OBOS5 13 0.292 0.285 0.370 + 1D204 OB6 14 0.029 0.742 0.370 + 1D204 OB7 15 0.292 0.629 0.370 + 1D204 OBOS8 16 0.029 0.172 0.370 + 1D204 OB9 17 0.009 0.457 0.796 + 1D204 OB10 18 0.272 0.000 0.796 + 1D204 OB11 19 0.333 0.457 0.164 + 1D204 OB12 20 0.069 0.000 0.164 + 1D204 OB13 21 0.401 0.686 0.814 + 1D204 OB14 22 0.137 0.229 0.814 + 1D204 OB15 23 0.401 0.229 0.814 + 1D204 OB16 24 0.137 0.686 0.814 + 1D204 OB17 25 0.468 0.686 0.146 + 1D204 OB18 26 0.204 0.229 0.146 + 1D204 OB19 27 0.468 0.229 0.146 + 1D204 OB20 28 0.204 0.686 0.146 + 1D204 FEO1 29 0.171 0.152 0.480 + 1D204 FEO2 30 0.434 0.609 0.480 + 1D204 FEO3 31 0.171 0.762 0.480 + 1D204 FE24 32 0.434 0.305 0.480 + 1D204 ST1 33 0.017 0.301 0.753 + 1D204 ST2 34 0.281 0.758 0.753 + 1D204 ST3 35 0.017 0.613 0.753 + 1D204 ST4 36 0.281 0.156 0.753 + 1D204 ST5 37 0.324 0.301 0.207 + 1D204 ST6 38 0.060 0.758 0.207 + 1D204 ST7 39 0.324 0.613 0.207 + 1D204 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2004.itp b/package/ClayCode/data/data/UCS/D21/D2004.itp new file mode 100644 index 00000000..3c15e939 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2004.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2004 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2004rtp D2004q -1.0 + 1 ho 1 D2004 HO1 1 0.425 1.008 + 2 ho 1 D2004 HO2 2 0.425 1.008 + 3 ho 1 D2004 HO3 3 0.425 1.008 + 4 ho 1 D2004 HO4 4 0.425 1.008 + 5 oh 1 D2004 OH1 5 -0.95 16 + 6 ohs 1 D2004 OHS2 6 -1.08083 16 ; OH on Oct Fe II + 7 oh 1 D2004 OH3 7 -0.95 16 + 8 ohs 1 D2004 OHS4 8 -1.08083 16 ; OH on Oct Fe II + 9 obos 1 D2004 OBOS1 9 -1.18084 16 ; OB on Oct Fe II + 10 ob 1 D2004 OB2 10 -1.05 16 + 11 ob 1 D2004 OB3 11 -1.05 16 + 12 obos 1 D2004 OBOS4 12 -1.18083 16 ; OB on Oct Fe II + 13 obos 1 D2004 OBOS5 13 -1.18084 16 ; OB on Oct Fe II + 14 ob 1 D2004 OB6 14 -1.05 16 + 15 ob 1 D2004 OB7 15 -1.05 16 + 16 obos 1 D2004 OBOS8 16 -1.18083 16 ; OB on Oct Fe II + 17 ob 1 D2004 OB9 17 -1.05 16 + 18 ob 1 D2004 OB10 18 -1.05 16 + 19 ob 1 D2004 OB11 19 -1.05 16 + 20 ob 1 D2004 OB12 20 -1.05 16 + 21 ob 1 D2004 OB13 21 -1.05 16 + 22 ob 1 D2004 OB14 22 -1.05 16 + 23 ob 1 D2004 OB15 23 -1.05 16 + 24 ob 1 D2004 OB16 24 -1.05 16 + 25 ob 1 D2004 OB17 25 -1.05 16 + 26 ob 1 D2004 OB18 26 -1.05 16 + 27 ob 1 D2004 OB19 27 -1.05 16 + 28 ob 1 D2004 OB20 28 -1.05 16 + 29 feo 1 D2004 FEO1 29 1.575 55.845 + 30 feo 1 D2004 FEO2 30 1.575 55.845 + 31 feo 1 D2004 FEO3 31 1.575 55.845 + 32 fe2 1 D2004 FE24 32 1.360 55.845 ; subs Oct Fe III + 33 st 1 D2004 ST1 33 2.1 28.09 + 34 st 1 D2004 ST2 34 2.1 28.09 + 35 st 1 D2004 ST3 35 2.1 28.09 + 36 st 1 D2004 ST4 36 2.1 28.09 + 37 st 1 D2004 ST5 37 2.1 28.09 + 38 st 1 D2004 ST6 38 2.1 28.09 + 39 st 1 D2004 ST7 39 2.1 28.09 + 40 st 1 D2004 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2005.gro b/package/ClayCode/data/data/UCS/D21/D2005.gro new file mode 100644 index 00000000..d5e37291 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2005.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 5 +40 + 1D205 HO1 1 0.183 0.000 0.583 + 1D205 HO2 2 0.447 0.457 0.583 + 1D205 HO3 3 0.158 0.000 0.377 + 1D205 HO4 4 0.422 0.457 0.377 + 1D205 OH1 5 0.084 0.000 0.583 + 1D205 OH2 6 0.348 0.457 0.583 + 1D205 OH3 7 0.257 0.000 0.377 + 1D205 OH4 8 -0.007 0.457 0.377 + 1D205 OB1 9 0.049 0.285 0.590 + 1D205 OB2 10 0.312 0.742 0.590 + 1D205 OB3 11 0.049 0.629 0.590 + 1D205 OB4 12 0.312 0.172 0.590 + 1D205 OB5 13 0.292 0.285 0.370 + 1D205 OB6 14 0.029 0.742 0.370 + 1D205 OB7 15 0.292 0.629 0.370 + 1D205 OB8 16 0.029 0.172 0.370 + 1D205 OB9 17 0.009 0.457 0.796 + 1D205 OB10 18 0.272 0.000 0.796 + 1D205 OB11 19 0.333 0.457 0.164 + 1D205 OB12 20 0.069 0.000 0.164 + 1D205 OB13 21 0.401 0.686 0.814 + 1D205 OB14 22 0.137 0.229 0.814 + 1D205 OB15 23 0.401 0.229 0.814 + 1D205 OB16 24 0.137 0.686 0.814 + 1D205 OB17 25 0.468 0.686 0.146 + 1D205 OB18 26 0.204 0.229 0.146 + 1D205 OB19 27 0.468 0.229 0.146 + 1D205 OB20 28 0.204 0.686 0.146 + 1D205 FEO1 29 0.171 0.152 0.480 + 1D205 AO2 30 0.434 0.609 0.480 + 1D205 FEO3 31 0.171 0.762 0.480 + 1D205 FEO4 32 0.434 0.305 0.480 + 1D205 ST1 33 0.017 0.301 0.753 + 1D205 ST2 34 0.281 0.758 0.753 + 1D205 ST3 35 0.017 0.613 0.753 + 1D205 ST4 36 0.281 0.156 0.753 + 1D205 ST5 37 0.324 0.301 0.207 + 1D205 ST6 38 0.060 0.758 0.207 + 1D205 ST7 39 0.324 0.613 0.207 + 1D205 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2005.itp b/package/ClayCode/data/data/UCS/D21/D2005.itp new file mode 100644 index 00000000..3f6fdd12 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2005.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2005 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2005rtp D2005q 0.0 + 1 ho 1 D2005 HO1 1 0.425 1.008 + 2 ho 1 D2005 HO2 2 0.425 1.008 + 3 ho 1 D2005 HO3 3 0.425 1.008 + 4 ho 1 D2005 HO4 4 0.425 1.008 + 5 oh 1 D2005 OH1 5 -0.95 16 + 6 oh 1 D2005 OH2 6 -0.95 16 + 7 oh 1 D2005 OH3 7 -0.95 16 + 8 oh 1 D2005 OH4 8 -0.95 16 + 9 ob 1 D2005 OB1 9 -1.05 16 + 10 ob 1 D2005 OB2 10 -1.05 16 + 11 ob 1 D2005 OB3 11 -1.05 16 + 12 ob 1 D2005 OB4 12 -1.05 16 + 13 ob 1 D2005 OB5 13 -1.05 16 + 14 ob 1 D2005 OB6 14 -1.05 16 + 15 ob 1 D2005 OB7 15 -1.05 16 + 16 ob 1 D2005 OB8 16 -1.05 16 + 17 ob 1 D2005 OB9 17 -1.05 16 + 18 ob 1 D2005 OB10 18 -1.05 16 + 19 ob 1 D2005 OB11 19 -1.05 16 + 20 ob 1 D2005 OB12 20 -1.05 16 + 21 ob 1 D2005 OB13 21 -1.05 16 + 22 ob 1 D2005 OB14 22 -1.05 16 + 23 ob 1 D2005 OB15 23 -1.05 16 + 24 ob 1 D2005 OB16 24 -1.05 16 + 25 ob 1 D2005 OB17 25 -1.05 16 + 26 ob 1 D2005 OB18 26 -1.05 16 + 27 ob 1 D2005 OB19 27 -1.05 16 + 28 ob 1 D2005 OB20 28 -1.05 16 + 29 feo 1 D2005 FEO1 29 1.575 55.845 + 30 ao 1 D2005 AO2 30 1.575 26.98 ; subs Oct Al + 31 feo 1 D2005 FEO3 31 1.575 55.845 + 32 feo 1 D2005 FEO4 32 1.575 55.845 + 33 st 1 D2005 ST1 33 2.1 28.09 + 34 st 1 D2005 ST2 34 2.1 28.09 + 35 st 1 D2005 ST3 35 2.1 28.09 + 36 st 1 D2005 ST4 36 2.1 28.09 + 37 st 1 D2005 ST5 37 2.1 28.09 + 38 st 1 D2005 ST6 38 2.1 28.09 + 39 st 1 D2005 ST7 39 2.1 28.09 + 40 st 1 D2005 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2006.gro b/package/ClayCode/data/data/UCS/D21/D2006.gro new file mode 100644 index 00000000..a93e7716 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2006.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 6 +40 + 1D206 HO1 1 0.183 0.000 0.583 + 1D206 HO2 2 0.447 0.457 0.583 + 1D206 HO3 3 0.158 0.000 0.377 + 1D206 HO4 4 0.422 0.457 0.377 + 1D206 OH1 5 0.084 0.000 0.583 + 1D206 OH2 6 0.348 0.457 0.583 + 1D206 OH3 7 0.257 0.000 0.377 + 1D206 OH4 8 -0.007 0.457 0.377 + 1D206 OB1 9 0.049 0.285 0.590 + 1D206 OB2 10 0.312 0.742 0.590 + 1D206 OB3 11 0.049 0.629 0.590 + 1D206 OB4 12 0.312 0.172 0.590 + 1D206 OB5 13 0.292 0.285 0.370 + 1D206 OB6 14 0.029 0.742 0.370 + 1D206 OB7 15 0.292 0.629 0.370 + 1D206 OB8 16 0.029 0.172 0.370 + 1D206 OB9 17 0.009 0.457 0.796 + 1D206 OB10 18 0.272 0.000 0.796 + 1D206 OB11 19 0.333 0.457 0.164 + 1D206 OB12 20 0.069 0.000 0.164 + 1D206 OB13 21 0.401 0.686 0.814 + 1D206 OB14 22 0.137 0.229 0.814 + 1D206 OB15 23 0.401 0.229 0.814 + 1D206 OB16 24 0.137 0.686 0.814 + 1D206 OB17 25 0.468 0.686 0.146 + 1D206 OB18 26 0.204 0.229 0.146 + 1D206 OB19 27 0.468 0.229 0.146 + 1D206 OB20 28 0.204 0.686 0.146 + 1D206 FEO1 29 0.171 0.152 0.480 + 1D206 FEO2 30 0.434 0.609 0.480 + 1D206 AO3 31 0.171 0.762 0.480 + 1D206 FEO4 32 0.434 0.305 0.480 + 1D206 ST1 33 0.017 0.301 0.753 + 1D206 ST2 34 0.281 0.758 0.753 + 1D206 ST3 35 0.017 0.613 0.753 + 1D206 ST4 36 0.281 0.156 0.753 + 1D206 ST5 37 0.324 0.301 0.207 + 1D206 ST6 38 0.060 0.758 0.207 + 1D206 ST7 39 0.324 0.613 0.207 + 1D206 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2006.itp b/package/ClayCode/data/data/UCS/D21/D2006.itp new file mode 100644 index 00000000..5b8a5266 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2006.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2006 1 + +[ atoms ] +; nr type resnr residue stom cgnr charge mass typeB chargeB massB +; residue 1 D2006rtp D2006q 0.0 + 1 ho 1 D2006 HO1 1 0.425 1.008 + 2 ho 1 D2006 HO2 2 0.425 1.008 + 3 ho 1 D2006 HO3 3 0.425 1.008 + 4 ho 1 D2006 HO4 4 0.425 1.008 + 5 oh 1 D2006 OH1 5 -0.95 16 + 6 oh 1 D2006 OH2 6 -0.95 16 + 7 oh 1 D2006 OH3 7 -0.95 16 + 8 oh 1 D2006 OH4 8 -0.95 16 + 9 ob 1 D2006 OB1 9 -1.05 16 + 10 ob 1 D2006 OB2 10 -1.05 16 + 11 ob 1 D2006 OB3 11 -1.05 16 + 12 ob 1 D2006 OB4 12 -1.05 16 + 13 ob 1 D2006 OB5 13 -1.05 16 + 14 ob 1 D2006 OB6 14 -1.05 16 + 15 ob 1 D2006 OB7 15 -1.05 16 + 16 ob 1 D2006 OB8 16 -1.05 16 + 17 ob 1 D2006 OB9 17 -1.05 16 + 18 ob 1 D2006 OB10 18 -1.05 16 + 19 ob 1 D2006 OB11 19 -1.05 16 + 20 ob 1 D2006 OB12 20 -1.05 16 + 21 ob 1 D2006 OB13 21 -1.05 16 + 22 ob 1 D2006 OB14 22 -1.05 16 + 23 ob 1 D2006 OB15 23 -1.05 16 + 24 ob 1 D2006 OB16 24 -1.05 16 + 25 ob 1 D2006 OB17 25 -1.05 16 + 26 ob 1 D2006 OB18 26 -1.05 16 + 27 ob 1 D2006 OB19 27 -1.05 16 + 28 ob 1 D2006 OB20 28 -1.05 16 + 29 feo 1 D2006 FEO1 29 1.575 55.845 + 30 feo 1 D2006 FEO2 30 1.575 55.845 + 31 ao 1 D2006 AO3 31 1.575 26.98 ; subs Oct Al + 32 feo 1 D2006 FEO4 32 1.575 55.845 + 33 st 1 D2006 ST1 33 2.1 26.98 + 34 st 1 D2006 ST2 34 2.1 28.09 + 35 st 1 D2006 ST3 35 2.1 28.09 + 36 st 1 D2006 ST4 36 2.1 28.09 + 37 st 1 D2006 ST5 37 2.1 28.09 + 38 st 1 D2006 ST6 38 2.1 28.09 + 39 st 1 D2006 ST7 39 2.1 28.09 + 40 st 1 D2006 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2007.gro b/package/ClayCode/data/data/UCS/D21/D2007.gro new file mode 100644 index 00000000..4a5df5ac --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2007.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 7 +40 + 1D207 HO1 1 0.183 0.000 0.583 + 1D207 HO2 2 0.447 0.457 0.583 + 1D207 HO3 3 0.158 0.000 0.377 + 1D207 HO4 4 0.422 0.457 0.377 + 1D207 OH1 5 0.084 0.000 0.583 + 1D207 OH2 6 0.348 0.457 0.583 + 1D207 OH3 7 0.257 0.000 0.377 + 1D207 OH4 8 -0.007 0.457 0.377 + 1D207 OBTS1 9 0.049 0.285 0.590 + 1D207 OB2 10 0.312 0.742 0.590 + 1D207 OB3 11 0.049 0.629 0.590 + 1D207 OB4 12 0.312 0.172 0.590 + 1D207 OB5 13 0.292 0.285 0.370 + 1D207 OB6 14 0.029 0.742 0.370 + 1D207 OB7 15 0.292 0.629 0.370 + 1D207 OB8 16 0.029 0.172 0.370 + 1D207 OBTS9 17 0.009 0.457 0.796 + 1D207 OB10 18 0.272 0.000 0.796 + 1D207 OB11 19 0.333 0.457 0.164 + 1D207 OB12 20 0.069 0.000 0.164 + 1D207 OB13 21 0.401 0.686 0.814 + 1D207 OBT14 22 0.137 0.229 0.814 + 1D207 OBT15 23 0.401 0.229 0.814 + 1D207 OB16 24 0.137 0.686 0.814 + 1D207 OB17 25 0.468 0.686 0.146 + 1D207 OB18 26 0.204 0.229 0.146 + 1D207 OB19 27 0.468 0.229 0.146 + 1D207 OB20 28 0.204 0.686 0.146 + 1D207 FEO1 29 0.171 0.152 0.480 + 1D207 FEO2 30 0.434 0.609 0.480 + 1D207 FEO3 31 0.171 0.762 0.480 + 1D207 FEO4 32 0.434 0.305 0.480 + 1D207 AT1 33 0.017 0.301 0.753 + 1D207 ST2 34 0.281 0.758 0.753 + 1D207 ST3 35 0.017 0.613 0.753 + 1D207 ST4 36 0.281 0.156 0.753 + 1D207 ST5 37 0.324 0.301 0.207 + 1D207 ST6 38 0.060 0.758 0.207 + 1D207 ST7 39 0.324 0.613 0.207 + 1D207 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2007.itp b/package/ClayCode/data/data/UCS/D21/D2007.itp new file mode 100644 index 00000000..aecabcfa --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2007.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2007 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2007rtp D2007q -1.0 + 1 ho 1 D2007 HO1 1 0.425 1.008 + 2 ho 1 D2007 HO2 2 0.425 1.008 + 3 ho 1 D2007 HO3 3 0.425 1.008 + 4 ho 1 D2007 HO4 4 0.425 1.008 + 5 oh 1 D2007 OH1 5 -0.95 16 + 6 oh 1 D2007 OH2 6 -0.95 16 + 7 oh 1 D2007 OH3 7 -0.95 16 + 8 oh 1 D2007 OH4 8 -0.95 16 + 9 obts 1 D2007 OBTS1 9 -1.16875 16 ; OB on Td Al + 10 ob 1 D2007 OB2 10 -1.05 16 + 11 ob 1 D2007 OB3 11 -1.05 16 + 12 ob 1 D2007 OB4 12 -1.05 16 + 13 ob 1 D2007 OB5 13 -1.05 16 + 14 ob 1 D2007 OB6 14 -1.05 16 + 15 ob 1 D2007 OB7 15 -1.05 16 + 16 ob 1 D2007 OB8 16 -1.05 16 + 17 obts 1 D2007 OBTS9 17 -1.16875 16 ; OB on Td Al + 18 ob 1 D2007 OB10 18 -1.05 16 + 19 ob 1 D2007 OB11 19 -1.05 16 + 20 ob 1 D2007 OB12 20 -1.05 16 + 21 ob 1 D2007 OB13 21 -1.05 16 + 22 obts 1 D2007 OBT14 22 -1.16875 16 ; OB on Td Al + 23 obts 1 D2007 OBT15 23 -1.16875 16 ; OB on Td Al + 24 ob 1 D2007 OB16 24 -1.05 16 + 25 ob 1 D2007 OB17 25 -1.05 16 + 26 ob 1 D2007 OB18 26 -1.05 16 + 27 ob 1 D2007 OB19 27 -1.05 16 + 28 ob 1 D2007 OB20 28 -1.05 16 + 29 feo 1 D2007 FEO1 29 1.575 55.845 + 30 feo 1 D2007 FEO2 30 1.575 55.845 + 31 feo 1 D2007 FEO3 31 1.575 55.845 + 32 feo 1 D2007 FEO4 32 1.575 55.845 + 33 at 1 D2007 AT1 33 1.575 26.98 ; subs Td Al + 34 st 1 D2007 ST2 34 2.1 28.09 + 35 st 1 D2007 ST3 35 2.1 28.09 + 36 st 1 D2007 ST4 36 2.1 28.09 + 37 st 1 D2007 ST5 37 2.1 28.09 + 38 st 1 D2007 ST6 38 2.1 28.09 + 39 st 1 D2007 ST7 39 2.1 28.09 + 40 st 1 D2007 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2008.gro b/package/ClayCode/data/data/UCS/D21/D2008.gro new file mode 100644 index 00000000..9b665397 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2008.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 8 +40 + 1D208 HO1 1 0.183 0.000 0.583 + 1D208 HO2 2 0.447 0.457 0.583 + 1D208 HO3 3 0.158 0.000 0.377 + 1D208 HO4 4 0.422 0.457 0.377 + 1D208 OH1 5 0.084 0.000 0.583 + 1D208 OH2 6 0.348 0.457 0.583 + 1D208 OH3 7 0.257 0.000 0.377 + 1D208 OH4 8 -0.007 0.457 0.377 + 1D208 OB1 9 0.049 0.285 0.590 + 1D208 OB2 10 0.312 0.742 0.590 + 1D208 OB3 11 0.049 0.629 0.590 + 1D208 OB4 12 0.312 0.172 0.590 + 1D208 OBTS5 13 0.292 0.285 0.370 + 1D208 OB6 14 0.029 0.742 0.370 + 1D208 OB7 15 0.292 0.629 0.370 + 1D208 OB8 16 0.029 0.172 0.370 + 1D208 OB9 17 0.009 0.457 0.796 + 1D208 OB10 18 0.272 0.000 0.796 + 1D208 OBT11 19 0.333 0.457 0.164 + 1D208 OB12 20 0.069 0.000 0.164 + 1D208 OB13 21 0.401 0.686 0.814 + 1D208 OB14 22 0.137 0.229 0.814 + 1D208 OB15 23 0.401 0.229 0.814 + 1D208 OB16 24 0.137 0.686 0.814 + 1D208 OB17 25 0.468 0.686 0.146 + 1D208 OBT18 26 0.204 0.229 0.146 + 1D208 OBT19 27 0.468 0.229 0.146 + 1D208 OB20 28 0.204 0.686 0.146 + 1D208 FEO1 29 0.171 0.152 0.480 + 1D208 FEO2 30 0.434 0.609 0.480 + 1D208 FEO3 31 0.171 0.762 0.480 + 1D208 FEO4 32 0.434 0.305 0.480 + 1D208 ST1 33 0.017 0.301 0.753 + 1D208 ST2 34 0.281 0.758 0.753 + 1D208 ST3 35 0.017 0.613 0.753 + 1D208 ST4 36 0.281 0.156 0.753 + 1D208 AT5 37 0.324 0.301 0.207 + 1D208 ST6 38 0.060 0.758 0.207 + 1D208 ST7 39 0.324 0.613 0.207 + 1D208 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2008.itp b/package/ClayCode/data/data/UCS/D21/D2008.itp new file mode 100644 index 00000000..35b01be5 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2008.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2008 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2008rtp D2008q -1.0 + 1 ho 1 D2008 HO1 1 0.425 1.008 + 2 ho 1 D2008 HO2 2 0.425 1.008 + 3 ho 1 D2008 HO3 3 0.425 1.008 + 4 ho 1 D2008 HO4 4 0.425 1.008 + 5 oh 1 D2008 OH1 5 -0.95 16 + 6 oh 1 D2008 OH2 6 -0.95 16 + 7 oh 1 D2008 OH3 7 -0.95 16 + 8 oh 1 D2008 OH4 8 -0.95 16 + 9 ob 1 D2008 OB1 9 -1.05 16 + 10 ob 1 D2008 OB2 10 -1.05 16 + 11 ob 1 D2008 OB3 11 -1.05 16 + 12 ob 1 D2008 OB4 12 -1.05 16 + 13 obts 1 D2008 OBTS5 13 -1.16875 16 ; OB on Td Al + 14 ob 1 D2008 OB6 14 -1.05 16 + 15 ob 1 D2008 OB7 15 -1.05 16 + 16 ob 1 D2008 OB8 16 -1.05 16 + 17 ob 1 D2008 OB9 17 -1.05 16 + 18 ob 1 D2008 OB10 18 -1.05 16 + 19 obts 1 D2008 OBT11 19 -1.16875 16 ; OB on Td Al + 20 ob 1 D2008 OB12 20 -1.05 16 + 21 ob 1 D2008 OB13 21 -1.05 16 + 22 ob 1 D2008 OB14 22 -1.05 16 + 23 ob 1 D2008 OB15 23 -1.05 16 + 24 ob 1 D2008 OB16 24 -1.05 16 + 25 ob 1 D2008 OB17 25 -1.05 16 + 26 obts 1 D2008 OBT18 26 -1.16875 16 ; OB on Td Al + 27 obts 1 D2008 OBT19 27 -1.16875 16 ; OB on Td Al + 28 ob 1 D2008 OB20 28 -1.05 16 + 29 feo 1 D2008 FEO1 29 1.575 55.845 + 30 feo 1 D2008 FEO2 30 1.575 55.845 + 31 feo 1 D2008 FEO3 31 1.575 55.845 + 32 feo 1 D2008 FEO4 32 1.575 55.845 + 33 st 1 D2008 ST1 33 2.1 26.98 + 34 st 1 D2008 ST2 34 2.1 28.09 + 35 st 1 D2008 ST3 35 2.1 28.09 + 36 st 1 D2008 ST4 36 2.1 28.09 + 37 at 1 D2008 AT5 37 1.575 26.98 ; subs Td Al + 38 st 1 D2008 ST6 38 2.1 28.09 + 39 st 1 D2008 ST7 39 2.1 28.09 + 40 st 1 D2008 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2009.gro b/package/ClayCode/data/data/UCS/D21/D2009.gro new file mode 100644 index 00000000..3d27187d --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2009.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 9 +40 + 1D209 HO1 1 0.183 0.000 0.583 + 1D209 HO2 2 0.447 0.457 0.583 + 1D209 HO3 3 0.158 0.000 0.377 + 1D209 HO4 4 0.422 0.457 0.377 + 1D209 OH1 5 0.084 0.000 0.583 + 1D209 OHS2 6 0.348 0.457 0.583 + 1D209 OH3 7 0.257 0.000 0.377 + 1D209 OHS4 8 -0.007 0.457 0.377 + 1D209 OBOS1 9 0.049 0.285 0.590 + 1D209 OB2 10 0.312 0.742 0.590 + 1D209 OB3 11 0.049 0.629 0.590 + 1D209 OBOS4 12 0.312 0.172 0.590 + 1D209 OBOS5 13 0.292 0.285 0.370 + 1D209 OB6 14 0.029 0.742 0.370 + 1D209 OB7 15 0.292 0.629 0.370 + 1D209 OBOS8 16 0.029 0.172 0.370 + 1D209 OB9 17 0.009 0.457 0.796 + 1D209 OB10 18 0.272 0.000 0.796 + 1D209 OB11 19 0.333 0.457 0.164 + 1D209 OB12 20 0.069 0.000 0.164 + 1D209 OB13 21 0.401 0.686 0.814 + 1D209 OB14 22 0.137 0.229 0.814 + 1D209 OB15 23 0.401 0.229 0.814 + 1D209 OB16 24 0.137 0.686 0.814 + 1D209 OB17 25 0.468 0.686 0.146 + 1D209 OB18 26 0.204 0.229 0.146 + 1D209 OB19 27 0.468 0.229 0.146 + 1D209 OB20 28 0.204 0.686 0.146 + 1D209 FEO1 29 0.171 0.152 0.480 + 1D209 FEO2 30 0.434 0.609 0.480 + 1D209 FEO3 31 0.171 0.762 0.480 + 1D209 MGO4 32 0.434 0.305 0.480 + 1D209 ST1 33 0.017 0.301 0.753 + 1D209 ST2 34 0.281 0.758 0.753 + 1D209 ST3 35 0.017 0.613 0.753 + 1D209 ST4 36 0.281 0.156 0.753 + 1D209 ST5 37 0.324 0.301 0.207 + 1D209 ST6 38 0.060 0.758 0.207 + 1D209 ST7 39 0.324 0.613 0.207 + 1D209 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2009.itp b/package/ClayCode/data/data/UCS/D21/D2009.itp new file mode 100644 index 00000000..f1fd3ed6 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2009.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2009 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2009rtp D2009q -1.0 + 1 ho 1 D2009 HO1 1 0.425 1.008 + 2 ho 1 D2009 HO2 2 0.425 1.008 + 3 ho 1 D2009 HO3 3 0.425 1.008 + 4 ho 1 D2009 HO4 4 0.425 1.008 + 5 oh 1 D2009 OH1 5 -0.95 16 + 6 ohs 1 D2009 OHS2 6 -1.08083 16 ; OH on Oct Mg + 7 oh 1 D2009 OH3 7 -0.95 16 + 8 ohs 1 D2009 OHS4 8 -1.08083 16 ; OH on Oct Mg + 9 obos 1 D2009 OBOS1 9 -1.18084 16 ; OB on Oct Mg + 10 ob 1 D2009 OB2 10 -1.05 16 + 11 ob 1 D2009 OB3 11 -1.05 16 + 12 obos 1 D2009 OBOS4 12 -1.18083 16 ; OB on Oct Mg + 13 obos 1 D2009 OBOS5 13 -1.18084 16 ; OB on Oct Mg + 14 ob 1 D2009 OB6 14 -1.05 16 + 15 ob 1 D2009 OB7 15 -1.05 16 + 16 obos 1 D2009 OBOS8 16 -1.18083 16 ; OB on Oct Mg + 17 ob 1 D2009 OB9 17 -1.05 16 + 18 ob 1 D2009 OB10 18 -1.05 16 + 19 ob 1 D2009 OB11 19 -1.05 16 + 20 ob 1 D2009 OB12 20 -1.05 16 + 21 ob 1 D2009 OB13 21 -1.05 16 + 22 ob 1 D2009 OB14 22 -1.05 16 + 23 ob 1 D2009 OB15 23 -1.05 16 + 24 ob 1 D2009 OB16 24 -1.05 16 + 25 ob 1 D2009 OB17 25 -1.05 16 + 26 ob 1 D2009 OB18 26 -1.05 16 + 27 ob 1 D2009 OB19 27 -1.05 16 + 28 ob 1 D2009 OB20 28 -1.05 16 + 29 feo 1 D2009 FEO1 29 1.575 55.845 + 30 feo 1 D2009 FEO2 30 1.575 55.845 + 31 feo 1 D2009 FEO3 31 1.575 55.845 + 32 mgo 1 D2009 MGO4 32 1.360 24.305 ; subs Oct Mg + 33 st 1 D2009 ST1 33 2.1 28.09 + 34 st 1 D2009 ST2 34 2.1 28.09 + 35 st 1 D2009 ST3 35 2.1 28.09 + 36 st 1 D2009 ST4 36 2.1 28.09 + 37 st 1 D2009 ST5 37 2.1 28.09 + 38 st 1 D2009 ST6 38 2.1 28.09 + 39 st 1 D2009 ST7 39 2.1 28.09 + 40 st 1 D2009 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2010.gro b/package/ClayCode/data/data/UCS/D21/D2010.gro new file mode 100644 index 00000000..c70ddccb --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2010.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 10 +40 + 1D210 HO1 1 0.183 0.000 0.583 + 1D210 HO2 2 0.447 0.457 0.583 + 1D210 HO3 3 0.158 0.000 0.377 + 1D210 HO4 4 0.422 0.457 0.377 + 1D210 OH1 5 0.084 0.000 0.583 + 1D210 OH2 6 0.348 0.457 0.583 + 1D210 OH3 7 0.257 0.000 0.377 + 1D210 OH4 8 -0.007 0.457 0.377 + 1D210 OBTS1 9 0.049 0.285 0.590 + 1D210 OB2 10 0.312 0.742 0.590 + 1D210 OB3 11 0.049 0.629 0.590 + 1D210 OB4 12 0.312 0.172 0.590 + 1D210 OB5 13 0.292 0.285 0.370 + 1D210 OB6 14 0.029 0.742 0.370 + 1D210 OB7 15 0.292 0.629 0.370 + 1D210 OB8 16 0.029 0.172 0.370 + 1D210 OBTS9 17 0.009 0.457 0.796 + 1D210 OB10 18 0.272 0.000 0.796 + 1D210 OB11 19 0.333 0.457 0.164 + 1D210 OB12 20 0.069 0.000 0.164 + 1D210 OB13 21 0.401 0.686 0.814 + 1D210 OBT14 22 0.137 0.229 0.814 + 1D210 OBT15 23 0.401 0.229 0.814 + 1D210 OB16 24 0.137 0.686 0.814 + 1D210 OB17 25 0.468 0.686 0.146 + 1D210 OB18 26 0.204 0.229 0.146 + 1D210 OB19 27 0.468 0.229 0.146 + 1D210 OB20 28 0.204 0.686 0.146 + 1D210 FEO1 29 0.171 0.152 0.480 + 1D210 AO2 30 0.434 0.609 0.480 + 1D210 FEO3 31 0.171 0.762 0.480 + 1D210 FEO4 32 0.434 0.305 0.480 + 1D210 FET1 33 0.017 0.301 0.753 + 1D210 ST2 34 0.281 0.758 0.753 + 1D210 ST3 35 0.017 0.613 0.753 + 1D210 ST4 36 0.281 0.156 0.753 + 1D210 ST5 37 0.324 0.301 0.207 + 1D210 ST6 38 0.060 0.758 0.207 + 1D210 ST7 39 0.324 0.613 0.207 + 1D210 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2010.itp b/package/ClayCode/data/data/UCS/D21/D2010.itp new file mode 100644 index 00000000..d89623b9 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2010.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2010 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2010rtp D202q -1.0 + 1 ho 1 D2010 HO1 1 0.425 1.008 + 2 ho 1 D2010 HO2 2 0.425 1.008 + 3 ho 1 D2010 HO3 3 0.425 1.008 + 4 ho 1 D2010 HO4 4 0.425 1.008 + 5 oh 1 D2010 OH1 5 -0.95 16 + 6 oh 1 D2010 OH2 6 -0.95 16 + 7 oh 1 D2010 OH3 7 -0.95 16 + 8 oh 1 D2010 OH4 8 -0.95 16 + 9 obts 1 D2010 OBTS1 9 -1.16875 16 ; OB on Td Fe + 10 ob 1 D2010 OB2 10 -1.05 16 + 11 ob 1 D2010 OB3 11 -1.05 16 + 12 ob 1 D2010 OB4 12 -1.05 16 + 13 ob 1 D2010 OB5 13 -1.05 16 + 14 ob 1 D2010 OB6 14 -1.05 16 + 15 ob 1 D2010 OB7 15 -1.05 16 + 16 ob 1 D2010 OB8 16 -1.05 16 + 17 obts 1 D2010 OBTS9 17 -1.16875 16 ; OB on Td Fe + 18 ob 1 D2010 OB10 18 -1.05 16 + 19 ob 1 D2010 OB11 19 -1.05 16 + 20 ob 1 D2010 OB12 20 -1.05 16 + 21 ob 1 D2010 OB13 21 -1.05 16 + 22 obts 1 D2010 OBT14 22 -1.16875 16 ; OB on Td Fe + 23 obts 1 D2010 OBT15 23 -1.16875 16 ; OB on Td Fe + 24 ob 1 D2010 OB16 24 -1.05 16 + 25 ob 1 D2010 OB17 25 -1.05 16 + 26 ob 1 D2010 OB18 26 -1.05 16 + 27 ob 1 D2010 OB19 27 -1.05 16 + 28 ob 1 D2010 OB20 28 -1.05 16 + 29 feo 1 D2010 FEO1 29 1.575 55.845 + 30 ao 1 D2010 AO2 30 1.575 26.98 ; subs Oct Al + 31 feo 1 D2010 FEO3 31 1.575 55.845 + 32 feo 1 D2010 FEO4 32 1.575 55.845 + 33 fet 1 D2010 FET1 33 1.575 55.845 ; subs Td Fe + 34 st 1 D2010 ST2 34 2.1 28.09 + 35 st 1 D2010 ST3 35 2.1 28.09 + 36 st 1 D2010 ST4 36 2.1 28.09 + 37 st 1 D2010 ST5 37 2.1 28.09 + 38 st 1 D2010 ST6 38 2.1 28.09 + 39 st 1 D2010 ST7 39 2.1 28.09 + 40 st 1 D2010 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2011.gro b/package/ClayCode/data/data/UCS/D21/D2011.gro new file mode 100644 index 00000000..1d756185 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2011.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 11 +40 + 1D211 HO1 1 0.183 0.000 0.583 + 1D211 HO2 2 0.447 0.457 0.583 + 1D211 HO3 3 0.158 0.000 0.377 + 1D211 HO4 4 0.422 0.457 0.377 + 1D211 OH1 5 0.084 0.000 0.583 + 1D211 OH2 6 0.348 0.457 0.583 + 1D211 OH3 7 0.257 0.000 0.377 + 1D211 OH4 8 -0.007 0.457 0.377 + 1D211 OB1 9 0.049 0.285 0.590 + 1D211 OB2 10 0.312 0.742 0.590 + 1D211 OB3 11 0.049 0.629 0.590 + 1D211 OB4 12 0.312 0.172 0.590 + 1D211 OBT5 13 0.292 0.285 0.370 + 1D211 OB6 14 0.029 0.742 0.370 + 1D211 OB7 15 0.292 0.629 0.370 + 1D211 OB8 16 0.029 0.172 0.370 + 1D211 OB9 17 0.009 0.457 0.796 + 1D211 OB10 18 0.272 0.000 0.796 + 1D211 OBT11 19 0.333 0.457 0.164 + 1D211 OB12 20 0.069 0.000 0.164 + 1D211 OB13 21 0.401 0.686 0.814 + 1D211 OB14 22 0.137 0.229 0.814 + 1D211 OB15 23 0.401 0.229 0.814 + 1D211 OB16 24 0.137 0.686 0.814 + 1D211 OB17 25 0.468 0.686 0.146 + 1D211 OBT18 26 0.204 0.229 0.146 + 1D211 OBT19 27 0.468 0.229 0.146 + 1D211 OB20 28 0.204 0.686 0.146 + 1D211 FEO1 29 0.171 0.152 0.480 + 1D211 FEO2 30 0.434 0.609 0.480 + 1D211 AO3 31 0.171 0.762 0.480 + 1D211 FEO4 32 0.434 0.305 0.480 + 1D211 ST1 33 0.017 0.301 0.753 + 1D211 ST2 34 0.281 0.758 0.753 + 1D211 ST3 35 0.017 0.613 0.753 + 1D211 ST4 36 0.281 0.156 0.753 + 1D211 FET5 37 0.324 0.301 0.207 + 1D211 ST6 38 0.060 0.758 0.207 + 1D211 ST7 39 0.324 0.613 0.207 + 1D211 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2011.itp b/package/ClayCode/data/data/UCS/D21/D2011.itp new file mode 100644 index 00000000..66e0b65a --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2011.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2011 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2011rtp D203q -1.0 + 1 ho 1 D2011 HO1 1 0.425 1.008 + 2 ho 1 D2011 HO2 2 0.425 1.008 + 3 ho 1 D2011 HO3 3 0.425 1.008 + 4 ho 1 D2011 HO4 4 0.425 1.008 + 5 oh 1 D2011 OH1 5 -0.95 16 + 6 oh 1 D2011 OH2 6 -0.95 16 + 7 oh 1 D2011 OH3 7 -0.95 16 + 8 oh 1 D2011 OH4 8 -0.95 16 + 9 ob 1 D2011 OB1 9 -1.05 16 + 10 ob 1 D2011 OB2 10 -1.05 16 + 11 ob 1 D2011 OB3 11 -1.05 16 + 12 ob 1 D2011 OB4 12 -1.05 16 + 13 obts 1 D2011 OBTS5 13 -1.16875 16 ; OB on Td Fe + 14 ob 1 D2011 OB6 14 -1.05 16 + 15 ob 1 D2011 OB7 15 -1.05 16 + 16 ob 1 D2011 OB8 16 -1.05 16 + 17 ob 1 D2011 OB9 17 -1.05 16 + 18 ob 1 D2011 OB10 18 -1.05 16 + 19 obts 1 D2011 OBT11 19 -1.16875 16 ; OB on Td Fe + 20 ob 1 D2011 OB12 20 -1.05 16 + 21 ob 1 D2011 OB13 21 -1.05 16 + 22 ob 1 D2011 OB14 22 -1.05 16 + 23 ob 1 D2011 OB15 23 -1.05 16 + 24 ob 1 D2011 OB16 24 -1.05 16 + 25 ob 1 D2011 OB17 25 -1.05 16 + 26 obts 1 D2011 OBT18 26 -1.16875 16 ; OB on Td Fe + 27 obts 1 D2011 OBT19 27 -1.16875 16 ; OB on Td Fe + 28 ob 1 D2011 OB20 28 -1.05 16 + 29 feo 1 D2011 FEO1 29 1.575 55.845 + 30 feo 1 D2011 FEO2 30 1.575 55.845 + 31 ao 1 D2011 AO3 31 1.575 26.98 ; subs Oct Al + 32 feo 1 D2011 FEO4 32 1.575 55.845 + 33 st 1 D2011 ST1 33 2.1 26.98 + 34 st 1 D2011 ST2 34 2.1 28.09 + 35 st 1 D2011 ST3 35 2.1 28.09 + 36 st 1 D2011 ST4 36 2.1 28.09 + 37 fet 1 D2011 FET5 37 1.575 55.845 ; subs Td Fe + 38 st 1 D2011 ST6 38 2.1 28.09 + 39 st 1 D2011 ST7 39 2.1 28.09 + 40 st 1 D2011 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2012.gro b/package/ClayCode/data/data/UCS/D21/D2012.gro new file mode 100644 index 00000000..aaef4ff4 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2012.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 12 +40 + 1D212 HO1 1 0.183 0.000 0.583 + 1D212 HO2 2 0.447 0.457 0.583 + 1D212 HO3 3 0.158 0.000 0.377 + 1D212 HO4 4 0.422 0.457 0.377 + 1D212 OH1 5 0.084 0.000 0.583 + 1D212 OH2 6 0.348 0.457 0.583 + 1D212 OH3 7 0.257 0.000 0.377 + 1D212 OH4 8 -0.007 0.457 0.377 + 1D212 OBTS1 9 0.049 0.285 0.590 + 1D212 OB2 10 0.312 0.742 0.590 + 1D212 OB3 11 0.049 0.629 0.590 + 1D212 OB4 12 0.312 0.172 0.590 + 1D212 OB5 13 0.292 0.285 0.370 + 1D212 OB6 14 0.029 0.742 0.370 + 1D212 OB7 15 0.292 0.629 0.370 + 1D212 OB8 16 0.029 0.172 0.370 + 1D212 OBTS9 17 0.009 0.457 0.796 + 1D212 OB10 18 0.272 0.000 0.796 + 1D212 OB11 19 0.333 0.457 0.164 + 1D212 OB12 20 0.069 0.000 0.164 + 1D212 OB13 21 0.401 0.686 0.814 + 1D212 OBT14 22 0.137 0.229 0.814 + 1D212 OBT15 23 0.401 0.229 0.814 + 1D212 OB16 24 0.137 0.686 0.814 + 1D212 OB17 25 0.468 0.686 0.146 + 1D212 OB18 26 0.204 0.229 0.146 + 1D212 OB19 27 0.468 0.229 0.146 + 1D212 OB20 28 0.204 0.686 0.146 + 1D212 FEO1 29 0.171 0.152 0.480 + 1D212 FEO2 30 0.434 0.609 0.480 + 1D212 FEO3 31 0.171 0.762 0.480 + 1D212 FEO4 32 0.434 0.305 0.480 + 1D212 FET1 33 0.017 0.301 0.753 + 1D212 ST2 34 0.281 0.758 0.753 + 1D212 ST3 35 0.017 0.613 0.753 + 1D212 ST4 36 0.281 0.156 0.753 + 1D212 ST5 37 0.324 0.301 0.207 + 1D212 ST6 38 0.060 0.758 0.207 + 1D212 ST7 39 0.324 0.613 0.207 + 1D212 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2012.itp b/package/ClayCode/data/data/UCS/D21/D2012.itp new file mode 100644 index 00000000..904127f0 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2012.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2012 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2012rtp D207q -1.0 + 1 ho 1 D2012 HO1 1 0.425 1.008 + 2 ho 1 D2012 HO2 2 0.425 1.008 + 3 ho 1 D2012 HO3 3 0.425 1.008 + 4 ho 1 D2012 HO4 4 0.425 1.008 + 5 oh 1 D2012 OH1 5 -0.95 16 + 6 oh 1 D2012 OH2 6 -0.95 16 + 7 oh 1 D2012 OH3 7 -0.95 16 + 8 oh 1 D2012 OH4 8 -0.95 16 + 9 obts 1 D2012 OBTS1 9 -1.16875 16 ; OB on Td Fe + 10 ob 1 D2012 OB2 10 -1.05 16 + 11 ob 1 D2012 OB3 11 -1.05 16 + 12 ob 1 D2012 OB4 12 -1.05 16 + 13 ob 1 D2012 OB5 13 -1.05 16 + 14 ob 1 D2012 OB6 14 -1.05 16 + 15 ob 1 D2012 OB7 15 -1.05 16 + 16 ob 1 D2012 OB8 16 -1.05 16 + 17 obts 1 D2012 OBTS9 17 -1.16875 16 ; OB on Td Fe + 18 ob 1 D2012 OB10 18 -1.05 16 + 19 ob 1 D2012 OB11 19 -1.05 16 + 20 ob 1 D2012 OB12 20 -1.05 16 + 21 ob 1 D2012 OB13 21 -1.05 16 + 22 obts 1 D2012 OBT14 22 -1.16875 16 ; OB on Td Fe + 23 obts 1 D2012 OBT15 23 -1.16875 16 ; OB on Td Fe + 24 ob 1 D2012 OB16 24 -1.05 16 + 25 ob 1 D2012 OB17 25 -1.05 16 + 26 ob 1 D2012 OB18 26 -1.05 16 + 27 ob 1 D2012 OB19 27 -1.05 16 + 28 ob 1 D2012 OB20 28 -1.05 16 + 29 feo 1 D2012 FEO1 29 1.575 55.845 + 30 feo 1 D2012 FEO2 30 1.575 55.845 + 31 feo 1 D2012 FEO3 31 1.575 55.845 + 32 feo 1 D2012 FEO4 32 1.575 55.845 + 33 fet 1 D2012 FET1 33 1.575 55.845 ; subs Td Fe + 34 st 1 D2012 ST2 34 2.1 28.09 + 35 st 1 D2012 ST3 35 2.1 28.09 + 36 st 1 D2012 ST4 36 2.1 28.09 + 37 st 1 D2012 ST5 37 2.1 28.09 + 38 st 1 D2012 ST6 38 2.1 28.09 + 39 st 1 D2012 ST7 39 2.1 28.09 + 40 st 1 D2012 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2013.gro b/package/ClayCode/data/data/UCS/D21/D2013.gro new file mode 100644 index 00000000..8f740e01 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2013.gro @@ -0,0 +1,44 @@ +Nontronite Unit Cell 13 +40 + 1D213 HO1 1 0.183 0.000 0.583 + 1D213 HO2 2 0.447 0.457 0.583 + 1D213 HO3 3 0.158 0.000 0.377 + 1D213 HO4 4 0.422 0.457 0.377 + 1D213 OH1 5 0.084 0.000 0.583 + 1D213 OH2 6 0.348 0.457 0.583 + 1D213 OH3 7 0.257 0.000 0.377 + 1D213 OH4 8 -0.007 0.457 0.377 + 1D213 OB1 9 0.049 0.285 0.590 + 1D213 OB2 10 0.312 0.742 0.590 + 1D213 OB3 11 0.049 0.629 0.590 + 1D213 OB4 12 0.312 0.172 0.590 + 1D213 OBTS5 13 0.292 0.285 0.370 + 1D213 OB6 14 0.029 0.742 0.370 + 1D213 OB7 15 0.292 0.629 0.370 + 1D213 OB8 16 0.029 0.172 0.370 + 1D213 OB9 17 0.009 0.457 0.796 + 1D213 OB10 18 0.272 0.000 0.796 + 1D213 OBT11 19 0.333 0.457 0.164 + 1D213 OB12 20 0.069 0.000 0.164 + 1D213 OB13 21 0.401 0.686 0.814 + 1D213 OB14 22 0.137 0.229 0.814 + 1D213 OB15 23 0.401 0.229 0.814 + 1D213 OB16 24 0.137 0.686 0.814 + 1D213 OB17 25 0.468 0.686 0.146 + 1D213 OBT18 26 0.204 0.229 0.146 + 1D213 OBT19 27 0.468 0.229 0.146 + 1D213 OB20 28 0.204 0.686 0.146 + 1D213 FEO1 29 0.171 0.152 0.480 + 1D213 FEO2 30 0.434 0.609 0.480 + 1D213 FEO3 31 0.171 0.762 0.480 + 1D213 FEO4 32 0.434 0.305 0.480 + 1D213 ST1 33 0.017 0.301 0.753 + 1D213 ST2 34 0.281 0.758 0.753 + 1D213 ST3 35 0.017 0.613 0.753 + 1D213 ST4 36 0.281 0.156 0.753 + 1D213 FET5 37 0.324 0.301 0.207 + 1D213 ST6 38 0.060 0.758 0.207 + 1D213 ST7 39 0.324 0.613 0.207 + 1D213 ST8 40 0.060 0.156 0.207 + 0.52770 0.91400 0.96003 0.00000 0.00000 0.00000 0.00000 -0.18661 0.00000 + diff --git a/package/ClayCode/data/data/UCS/D21/D2013.itp b/package/ClayCode/data/data/UCS/D21/D2013.itp new file mode 100644 index 00000000..f5a0ae56 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2013.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2013 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2013rtp D208q -1.0 + 1 ho 1 D2013 HO1 1 0.425 1.008 + 2 ho 1 D2013 HO2 2 0.425 1.008 + 3 ho 1 D2013 HO3 3 0.425 1.008 + 4 ho 1 D2013 HO4 4 0.425 1.008 + 5 oh 1 D2013 OH1 5 -0.95 16 + 6 oh 1 D2013 OH2 6 -0.95 16 + 7 oh 1 D2013 OH3 7 -0.95 16 + 8 oh 1 D2013 OH4 8 -0.95 16 + 9 ob 1 D2013 OB1 9 -1.05 16 + 10 ob 1 D2013 OB2 10 -1.05 16 + 11 ob 1 D2013 OB3 11 -1.05 16 + 12 ob 1 D2013 OB4 12 -1.05 16 + 13 obts 1 D2013 OBTS5 13 -1.16875 16 ; OB on Td Fe + 14 ob 1 D2013 OB6 14 -1.05 16 + 15 ob 1 D2013 OB7 15 -1.05 16 + 16 ob 1 D2013 OB8 16 -1.05 16 + 17 ob 1 D2013 OB9 17 -1.05 16 + 18 ob 1 D2013 OB10 18 -1.05 16 + 19 obts 1 D2013 OBT11 19 -1.16875 16 ; OB on Td Fe + 20 ob 1 D2013 OB12 20 -1.05 16 + 21 ob 1 D2013 OB13 21 -1.05 16 + 22 ob 1 D2013 OB14 22 -1.05 16 + 23 ob 1 D2013 OB15 23 -1.05 16 + 24 ob 1 D2013 OB16 24 -1.05 16 + 25 ob 1 D2013 OB17 25 -1.05 16 + 26 obts 1 D2013 OBT18 26 -1.16875 16 ; OB on Td Fe + 27 obts 1 D2013 OBT19 27 -1.16875 16 ; OB on Td Fe + 28 ob 1 D2013 OB20 28 -1.05 16 + 29 feo 1 D2013 FEO1 29 1.575 55.845 + 30 feo 1 D2013 FEO2 30 1.575 55.845 + 31 feo 1 D2013 FEO3 31 1.575 55.845 + 32 feo 1 D2013 FEO4 32 1.575 55.845 + 33 st 1 D2013 ST1 33 2.1 26.98 + 34 st 1 D2013 ST2 34 2.1 28.09 + 35 st 1 D2013 ST3 35 2.1 28.09 + 36 st 1 D2013 ST4 36 2.1 28.09 + 37 fet 1 D2013 FET5 37 1.575 55.845 ; subs Td fe + 38 st 1 D2013 ST6 38 2.1 28.09 + 39 st 1 D2013 ST7 39 2.1 28.09 + 40 st 1 D2013 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2020.gro b/package/ClayCode/data/data/UCS/D21/D2020.gro new file mode 100644 index 00000000..c6ca4de4 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2020.gro @@ -0,0 +1,45 @@ +cis-vacant dioctahedral smectite, Montmorillonite, AMCSD: 0002868 +40 + 1D220 HO1 1 0.084 0.120 0.595 + 1D220 HO2 2 0.181 0.230 0.205 + 1D220 HO3 3 0.441 0.679 0.205 + 1D220 HO4 4 0.344 0.568 0.595 + 1D220 OH1 5 0.101 0.122 0.499 + 1D220 OH2 6 0.163 0.228 0.301 + 1D220 OH3 7 0.424 0.677 0.301 + 1D220 OH4 8 0.362 0.570 0.499 + 1D220 OB1 9 0.317 0.847 0.506 + 1D220 OB2 10 0.361 0.225 0.507 + 1D220 OB3 11 0.463 0.400 0.294 + 1D220 OB4 12 0.419 0.125 0.294 + 1D220 OB5 13 0.202 0.848 0.294 + 1D220 OB6 14 0.164 0.574 0.294 + 1D220 OB7 15 0.062 0.399 0.506 + 1D220 OB8 16 0.106 0.673 0.507 + 1D220 OB9 17 0.485 0.293 0.730 + 1D220 OB10 18 0.316 0.091 0.729 + 1D220 OB11 19 0.229 0.342 0.706 + 1D220 OB12 20 0.295 0.057 0.070 + 1D220 OB13 21 0.464 0.259 0.071 + 1D220 OB14 22 0.035 0.008 0.095 + 1D220 OB15 23 0.040 0.505 0.070 + 1D220 OB16 24 0.209 0.707 0.071 + 1D220 OB17 25 0.296 0.457 0.095 + 1D220 OB18 26 0.229 0.742 0.730 + 1D220 OB19 27 0.061 0.539 0.729 + 1D220 OB20 28 0.490 0.790 0.706 + 1D220 AO1 29 0.260 0.101 0.400 + 1D220 AO2 30 0.004 0.249 0.400 + 1D220 AO3 31 0.265 0.698 0.400 + 1D220 AO4 32 0.005 0.549 0.400 + 1D220 ST1 33 0.336 0.840 0.668 + 1D220 ST2 34 0.346 0.238 0.669 + 1D220 ST3 35 0.444 0.407 0.132 + 1D220 ST4 36 0.434 0.112 0.131 + 1D220 ST5 37 0.183 0.856 0.132 + 1D220 ST6 38 0.179 0.561 0.131 + 1D220 ST7 39 0.081 0.391 0.668 + 1D220 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + + diff --git a/package/ClayCode/data/data/UCS/D21/D2020.itp b/package/ClayCode/data/data/UCS/D21/D2020.itp new file mode 100644 index 00000000..5a5d4e41 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2020.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2020 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2020rtp D2020 q 0.0 + 1 ho 1 D2020 HO1 1 0.425 1.008 + 2 ho 1 D2020 HO2 2 0.425 1.008 + 3 ho 1 D2020 HO3 3 0.425 1.008 + 4 ho 1 D2020 HO4 4 0.425 1.008 + 5 oh 1 D2020 OH1 5 -0.95 16 + 6 oh 1 D2020 OH2 6 -0.95 16 + 7 oh 1 D2020 OH3 7 -0.95 16 + 8 oh 1 D2020 OH4 8 -0.95 16 + 9 ob 1 D2020 OB1 9 -1.05 16 + 10 ob 1 D2020 OB2 10 -1.05 16 + 11 ob 1 D2020 OB3 11 -1.05 16 + 12 ob 1 D2020 OB4 12 -1.05 16 + 13 ob 1 D2020 OB5 13 -1.05 16 + 14 ob 1 D2020 OB6 14 -1.05 16 + 15 ob 1 D2020 OB7 15 -1.05 16 + 16 ob 1 D2020 OB8 16 -1.05 16 + 17 ob 1 D2020 OB9 17 -1.05 16 + 18 ob 1 D2020 OB10 18 -1.05 16 + 19 ob 1 D2020 OB11 19 -1.05 16 + 20 ob 1 D2020 OB12 20 -1.05 16 + 21 ob 1 D2020 OB13 21 -1.05 16 + 22 ob 1 D2020 OB14 22 -1.05 16 + 23 ob 1 D2020 OB15 23 -1.05 16 + 24 ob 1 D2020 OB16 24 -1.05 16 + 25 ob 1 D2020 OB17 25 -1.05 16 + 26 ob 1 D2020 OB18 26 -1.05 16 + 27 ob 1 D2020 OB19 27 -1.05 16 + 28 ob 1 D2020 OB20 28 -1.05 16 + 29 ao 1 D2020 AO1 29 1.575 26.98 + 30 ao 1 D2020 AO2 30 1.575 26.98 + 31 ao 1 D2020 AO3 31 1.575 26.98 + 32 ao 1 D2020 AO4 32 1.575 26.98 + 33 st 1 D2020 ST1 33 2.1 28.09 + 34 st 1 D2020 ST2 34 2.1 28.09 + 35 st 1 D2020 ST3 35 2.1 28.09 + 36 st 1 D2020 ST4 36 2.1 28.09 + 37 st 1 D2020 ST5 37 2.1 28.09 + 38 st 1 D2020 ST6 38 2.1 28.09 + 39 st 1 D2020 ST7 39 2.1 28.09 + 40 st 1 D2020 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2021.gro b/package/ClayCode/data/data/UCS/D21/D2021.gro new file mode 100644 index 00000000..a47e463b --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2021.gro @@ -0,0 +1,45 @@ +Smectite Unit Cell 2 x Oct Fe3 +40 + 1D221 HO1 1 0.084 0.120 0.595 + 1D221 HO2 2 0.181 0.230 0.205 + 1D221 HO3 3 0.441 0.679 0.205 + 1D221 HO4 4 0.344 0.568 0.595 + 1D221 OH1 5 0.101 0.122 0.499 + 1D221 OH2 6 0.163 0.228 0.301 + 1D221 OH3 7 0.424 0.677 0.301 + 1D221 OH4 8 0.362 0.570 0.499 + 1D221 OB1 9 0.317 0.847 0.506 + 1D221 OB2 10 0.361 0.225 0.507 + 1D221 OB3 11 0.463 0.400 0.294 + 1D221 OB4 12 0.419 0.125 0.294 + 1D221 OB5 13 0.202 0.848 0.294 + 1D221 OB6 14 0.164 0.574 0.294 + 1D221 OB7 15 0.062 0.399 0.506 + 1D221 OB8 16 0.106 0.673 0.507 + 1D221 OB9 17 0.485 0.293 0.730 + 1D221 OB10 18 0.316 0.091 0.729 + 1D221 OB11 19 0.229 0.342 0.706 + 1D221 OB12 20 0.295 0.057 0.070 + 1D221 OB13 21 0.464 0.259 0.071 + 1D221 OB14 22 0.035 0.008 0.095 + 1D221 OB15 23 0.040 0.505 0.070 + 1D221 OB16 24 0.209 0.707 0.071 + 1D221 OB17 25 0.296 0.457 0.095 + 1D221 OB18 26 0.229 0.742 0.730 + 1D221 OB19 27 0.061 0.539 0.729 + 1D221 OB20 28 0.490 0.790 0.706 + 1D221 FO1 29 0.260 0.101 0.400 + 1D221 AO2 30 0.004 0.249 0.400 + 1D221 AO3 31 0.265 0.698 0.400 + 1D221 FO4 32 0.005 0.549 0.400 + 1D221 ST1 33 0.336 0.840 0.668 + 1D221 ST2 34 0.346 0.238 0.669 + 1D221 ST3 35 0.444 0.407 0.132 + 1D221 ST4 36 0.434 0.112 0.131 + 1D221 ST5 37 0.183 0.856 0.132 + 1D221 ST6 38 0.179 0.561 0.131 + 1D221 ST7 39 0.081 0.391 0.668 + 1D221 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + + diff --git a/package/ClayCode/data/data/UCS/D21/D2021.itp b/package/ClayCode/data/data/UCS/D21/D2021.itp new file mode 100644 index 00000000..e414c314 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2021.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2021 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2021rtp D2021 q 0.0 + 1 ho 1 D2021 HO1 1 0.425 1.008 + 2 ho 1 D2021 HO2 2 0.425 1.008 + 3 ho 1 D2021 HO3 3 0.425 1.008 + 4 ho 1 D2021 HO4 4 0.425 1.008 + 5 oh 1 D2021 OH1 5 -0.95 16 + 6 oh 1 D2021 OH2 6 -0.95 16 + 7 oh 1 D2021 OH3 7 -0.95 16 + 8 oh 1 D2021 OH4 8 -0.95 16 + 9 ob 1 D2021 OB1 9 -1.05 16 + 10 ob 1 D2021 OB2 10 -1.05 16 + 11 ob 1 D2021 OB3 11 -1.05 16 + 12 ob 1 D2021 OB4 12 -1.05 16 + 13 ob 1 D2021 OB5 13 -1.05 16 + 14 ob 1 D2021 OB6 14 -1.05 16 + 15 ob 1 D2021 OB7 15 -1.05 16 + 16 ob 1 D2021 OB8 16 -1.05 16 + 17 ob 1 D2021 OB9 17 -1.05 16 + 18 ob 1 D2021 OB10 18 -1.05 16 + 19 ob 1 D2021 OB11 19 -1.05 16 + 20 ob 1 D2021 OB12 20 -1.05 16 + 21 ob 1 D2021 OB13 21 -1.05 16 + 22 ob 1 D2021 OB14 22 -1.05 16 + 23 ob 1 D2021 OB15 23 -1.05 16 + 24 ob 1 D2021 OB16 24 -1.05 16 + 25 ob 1 D2021 OB17 25 -1.05 16 + 26 ob 1 D2021 OB18 26 -1.05 16 + 27 ob 1 D2021 OB19 27 -1.05 16 + 28 ob 1 D2021 OB20 28 -1.05 16 + 29 feo 1 D2021 FO1 29 1.575 55.85 ; subst Fe III + 30 ao 1 D2021 AO2 30 1.575 26.98 + 31 ao 1 D2021 AO3 31 1.575 26.98 + 32 feo 1 D2021 FO4 32 1.575 55.85 ; subst Fe III + 33 st 1 D2021 ST1 33 2.1 28.09 + 34 st 1 D2021 ST2 34 2.1 28.09 + 35 st 1 D2021 ST3 35 2.1 28.09 + 36 st 1 D2021 ST4 36 2.1 28.09 + 37 st 1 D2021 ST5 37 2.1 28.09 + 38 st 1 D2021 ST6 38 2.1 28.09 + 39 st 1 D2021 ST7 39 2.1 28.09 + 40 st 1 D2021 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2022.gro b/package/ClayCode/data/data/UCS/D21/D2022.gro new file mode 100644 index 00000000..151a407c --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2022.gro @@ -0,0 +1,44 @@ +Smectite Unit Cell 1 x Oct Mg +40 + 1D222 HO1 1 0.084 0.120 0.595 + 1D222 HO2 2 0.181 0.230 0.205 + 1D222 HO3 3 0.441 0.679 0.205 + 1D222 HO4 4 0.344 0.568 0.595 + 1D222 OH1 5 0.101 0.122 0.499 + 1D222 OH2 6 0.163 0.228 0.301 + 1D222 OHS3 7 0.424 0.677 0.301 + 1D222 OHS4 8 0.362 0.570 0.499 + 1D222 OBS1 9 0.317 0.847 0.506 + 1D222 OB2 10 0.361 0.225 0.507 + 1D222 OB3 11 0.463 0.400 0.294 + 1D222 OB4 12 0.419 0.125 0.294 + 1D222 OBS5 13 0.202 0.848 0.294 + 1D222 OBS6 14 0.164 0.574 0.294 + 1D222 OB7 15 0.062 0.399 0.506 + 1D222 OBS8 16 0.106 0.673 0.507 + 1D222 OB9 17 0.485 0.293 0.730 + 1D222 OB10 18 0.316 0.091 0.729 + 1D222 OB11 19 0.229 0.342 0.706 + 1D222 OB12 20 0.295 0.057 0.070 + 1D222 OB13 21 0.464 0.259 0.071 + 1D222 OB14 22 0.035 0.008 0.095 + 1D222 OB15 23 0.040 0.505 0.070 + 1D222 OB16 24 0.209 0.707 0.071 + 1D222 OB17 25 0.296 0.457 0.095 + 1D222 OB18 26 0.229 0.742 0.730 + 1D222 OB19 27 0.061 0.539 0.729 + 1D222 OB20 28 0.490 0.790 0.706 + 1D222 AO1 29 0.260 0.101 0.400 + 1D222 AO2 30 0.004 0.249 0.400 + 1D222 MGO3 31 0.265 0.698 0.400 + 1D222 AO4 32 0.005 0.549 0.400 + 1D222 ST1 33 0.336 0.840 0.668 + 1D222 ST2 34 0.346 0.238 0.669 + 1D222 ST3 35 0.444 0.407 0.132 + 1D222 ST4 36 0.434 0.112 0.131 + 1D222 ST5 37 0.183 0.856 0.132 + 1D222 ST6 38 0.179 0.561 0.131 + 1D222 ST7 39 0.081 0.391 0.668 + 1D222 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + diff --git a/package/ClayCode/data/data/UCS/D21/D2022.itp b/package/ClayCode/data/data/UCS/D21/D2022.itp new file mode 100644 index 00000000..e9e81081 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2022.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2022 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2022rtp D2022 q -1 + 1 ho 1 D2022 HO1 1 0.425 1.008 + 2 ho 1 D2022 HO2 2 0.425 1.008 + 3 ho 1 D2022 HO3 3 0.425 1.008 + 4 ho 1 D2022 HO4 4 0.425 1.008 + 5 oh 1 D2022 OH1 5 -0.95 16 + 6 oh 1 D2022 OH2 6 -0.95 16 + 7 ohs 1 D2022 OHS3 7 -1.0808 16 ; OH on Mg + 8 ohs 1 D2022 OHS4 8 -1.0808 16 ; OH on Mg + 9 obos 1 D2022 OBS1 9 -1.1808 16 ; Ob on Mg + 10 ob 1 D2022 OB2 10 -1.05 16 + 11 ob 1 D2022 OB3 11 -1.05 16 + 12 ob 1 D2022 OB4 12 -1.05 16 + 13 obos 1 D2022 OBS5 13 -1.1808 16 ; Ob on Mg + 14 obos 1 D2022 OBS6 14 -1.1808 16 ; Ob on Mg + 15 ob 1 D2022 OB7 15 -1.05 16 + 16 obos 1 D2022 OBS8 16 -1.1808 16 ; Ob on Mg + 17 ob 1 D2022 OB9 17 -1.05 16 + 18 ob 1 D2022 OB10 18 -1.05 16 + 19 ob 1 D2022 OB11 19 -1.05 16 + 20 ob 1 D2022 OB12 20 -1.05 16 + 21 ob 1 D2022 OB13 21 -1.05 16 + 22 ob 1 D2022 OB14 22 -1.05 16 + 23 ob 1 D2022 OB15 23 -1.05 16 + 24 ob 1 D2022 OB16 24 -1.05 16 + 25 ob 1 D2022 OB17 25 -1.05 16 + 26 ob 1 D2022 OB18 26 -1.05 16 + 27 ob 1 D2022 OB19 27 -1.05 16 + 28 ob 1 D2022 OB20 28 -1.05 16 + 29 ao 1 D2022 AO1 29 1.575 26.98 + 30 ao 1 D2022 AO2 30 1.575 26.98 + 31 mgo 1 D2022 MGO3 31 1.3598 24.31 ; subst Mg + 32 ao 1 D2022 AO4 32 1.575 26.98 + 33 st 1 D2022 ST1 33 2.1 28.09 + 34 st 1 D2022 ST2 34 2.1 28.09 + 35 st 1 D2022 ST3 35 2.1 28.09 + 36 st 1 D2022 ST4 36 2.1 28.09 + 37 st 1 D2022 ST5 37 2.1 28.09 + 38 st 1 D2022 ST6 38 2.1 28.09 + 39 st 1 D2022 ST7 39 2.1 28.09 + 40 st 1 D2022 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2023.gro b/package/ClayCode/data/data/UCS/D21/D2023.gro new file mode 100644 index 00000000..bd897d17 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2023.gro @@ -0,0 +1,44 @@ +Smectite Unit Cell 1 x Td Al +40 + 1D223 HO1 1 0.084 0.120 0.595 + 1D223 HO2 2 0.181 0.230 0.205 + 1D223 HO3 3 0.441 0.679 0.205 + 1D223 HO4 4 0.344 0.568 0.595 + 1D223 OH1 5 0.101 0.122 0.499 + 1D223 OH2 6 0.163 0.228 0.301 + 1D223 OH3 7 0.424 0.677 0.301 + 1D223 OH4 8 0.362 0.570 0.499 + 1D223 OB1 9 0.317 0.847 0.506 + 1D223 OB2 10 0.361 0.225 0.507 + 1D223 OB3 11 0.463 0.400 0.294 + 1D223 OB4 12 0.419 0.125 0.294 + 1D223 OB5 13 0.202 0.848 0.294 + 1D223 OBT6 14 0.164 0.574 0.294 + 1D223 OB7 15 0.062 0.399 0.506 + 1D223 OB8 16 0.106 0.673 0.507 + 1D223 OB9 17 0.485 0.293 0.730 + 1D223 OB10 18 0.316 0.091 0.729 + 1D223 OB11 19 0.229 0.342 0.706 + 1D223 OB12 20 0.295 0.057 0.070 + 1D223 OB13 21 0.464 0.259 0.071 + 1D223 OB14 22 0.035 0.008 0.095 + 1D223 OBT15 23 0.040 0.505 0.070 + 1D223 OBT16 24 0.209 0.707 0.071 + 1D223 OBT17 25 0.296 0.457 0.095 + 1D223 OB18 26 0.229 0.742 0.730 + 1D223 OB19 27 0.061 0.539 0.729 + 1D223 OB20 28 0.490 0.790 0.706 + 1D223 AO1 29 0.260 0.101 0.400 + 1D223 AO2 30 0.004 0.249 0.400 + 1D223 AO3 31 0.265 0.698 0.400 + 1D223 AO4 32 0.005 0.549 0.400 + 1D223 ST1 33 0.336 0.840 0.668 + 1D223 ST2 34 0.346 0.238 0.669 + 1D223 ST3 35 0.444 0.407 0.132 + 1D223 ST4 36 0.434 0.112 0.131 + 1D223 ST5 37 0.183 0.856 0.132 + 1D223 AT6 38 0.179 0.561 0.131 + 1D223 ST7 39 0.081 0.391 0.668 + 1D223 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + diff --git a/package/ClayCode/data/data/UCS/D21/D2023.itp b/package/ClayCode/data/data/UCS/D21/D2023.itp new file mode 100644 index 00000000..820fc753 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2023.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2023 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2023rtp D2023 q -1.0 + 1 ho 1 D2023 HO1 1 0.425 1.008 + 2 ho 1 D2023 HO2 2 0.425 1.008 + 3 ho 1 D2023 HO3 3 0.425 1.008 + 4 ho 1 D2023 HO4 4 0.425 1.008 + 5 oh 1 D2023 OH1 5 -0.95 16 + 6 oh 1 D2023 OH2 6 -0.95 16 + 7 oh 1 D2023 OH3 7 -0.95 16 + 8 oh 1 D2023 OH4 8 -0.95 16 + 9 ob 1 D2023 OB1 9 -1.05 16 + 10 ob 1 D2023 OB2 10 -1.05 16 + 11 ob 1 D2023 OB3 11 -1.05 16 + 12 ob 1 D2023 OB4 12 -1.05 16 + 13 ob 1 D2023 OB5 13 -1.05 16 + 14 obts 1 D2023 OBT6 14 -1.16875 16 ; Ob on Td Al + 15 ob 1 D2023 OB7 15 -1.05 16 + 16 ob 1 D2023 OB8 16 -1.05 16 + 17 ob 1 D2023 OB9 17 -1.05 16 + 18 ob 1 D2023 OB10 18 -1.05 16 + 19 ob 1 D2023 OB11 19 -1.05 16 + 20 ob 1 D2023 OB12 20 -1.05 16 + 21 ob 1 D2023 OB13 21 -1.05 16 + 22 ob 1 D2023 OB14 22 -1.05 16 + 23 obts 1 D2023 OBT15 23 -1.16875 16 ; Ob on Td Al + 24 obts 1 D2023 OBT16 24 -1.16875 16 ; Ob on Td Al + 25 obts 1 D2023 OBT17 25 -1.16875 16 ; Ob on Td Al + 26 ob 1 D2023 OB18 26 -1.05 16 + 27 ob 1 D2023 OB19 27 -1.05 16 + 28 ob 1 D2023 OB20 28 -1.05 16 + 29 ao 1 D2023 AO1 29 1.575 26.98 + 30 ao 1 D2023 AO2 30 1.575 26.98 + 31 ao 1 D2023 AO3 31 1.575 26.98 + 32 ao 1 D2023 AO4 32 1.575 26.98 + 33 st 1 D2023 ST1 33 2.1 28.09 + 34 st 1 D2023 ST2 34 2.1 28.09 + 35 st 1 D2023 ST3 35 2.1 28.09 + 36 st 1 D2023 ST4 36 2.1 28.09 + 37 st 1 D2023 ST5 37 2.1 28.09 + 38 at 1 D2023 AT6 38 1.575 26.98 ; subst to Td Al + 39 st 1 D2023 ST7 39 2.1 28.09 + 40 st 1 D2023 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2024.gro b/package/ClayCode/data/data/UCS/D21/D2024.gro new file mode 100644 index 00000000..7569ccfc --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2024.gro @@ -0,0 +1,44 @@ +Smectite Unit Cell 1 x Td Al +40 + 1D224 HO1 1 0.084 0.120 0.595 + 1D224 HO2 2 0.181 0.230 0.205 + 1D224 HO3 3 0.441 0.679 0.205 + 1D224 HO4 4 0.344 0.568 0.595 + 1D224 OH1 5 0.101 0.122 0.499 + 1D224 OH2 6 0.163 0.228 0.301 + 1D224 OH3 7 0.424 0.677 0.301 + 1D224 OH4 8 0.362 0.570 0.499 + 1D224 OB1 9 0.317 0.847 0.506 + 1D224 OBT2 10 0.361 0.225 0.507 + 1D224 OB3 11 0.463 0.400 0.294 + 1D224 OB4 12 0.419 0.125 0.294 + 1D224 OB5 13 0.202 0.848 0.294 + 1D224 OB6 14 0.164 0.574 0.294 + 1D224 OB7 15 0.062 0.399 0.506 + 1D224 OB8 16 0.106 0.673 0.507 + 1D224 OBT9 17 0.485 0.293 0.730 + 1D224 OBT10 18 0.316 0.091 0.729 + 1D224 OBT11 19 0.229 0.342 0.706 + 1D224 OB12 20 0.295 0.057 0.070 + 1D224 OB13 21 0.464 0.259 0.071 + 1D224 OB14 22 0.035 0.008 0.095 + 1D224 OB15 23 0.040 0.505 0.070 + 1D224 OB16 24 0.209 0.707 0.071 + 1D224 OB17 25 0.296 0.457 0.095 + 1D224 OB18 26 0.229 0.742 0.730 + 1D224 OB19 27 0.061 0.539 0.729 + 1D224 OB20 28 0.490 0.790 0.706 + 1D224 AO1 29 0.260 0.101 0.400 + 1D224 AO2 30 0.004 0.249 0.400 + 1D224 AO3 31 0.265 0.698 0.400 + 1D224 AO4 32 0.005 0.549 0.400 + 1D224 ST1 33 0.336 0.840 0.668 + 1D224 AT2 34 0.346 0.238 0.669 + 1D224 ST3 35 0.444 0.407 0.132 + 1D224 ST4 36 0.434 0.112 0.131 + 1D224 ST5 37 0.183 0.856 0.132 + 1D224 ST6 38 0.179 0.561 0.131 + 1D224 ST7 39 0.081 0.391 0.668 + 1D224 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + diff --git a/package/ClayCode/data/data/UCS/D21/D2024.itp b/package/ClayCode/data/data/UCS/D21/D2024.itp new file mode 100644 index 00000000..07869ba0 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2024.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2024 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2024rtp D2024 q -1.0 + 1 ho 1 D2024 HO1 1 0.425 1.008 + 2 ho 1 D2024 HO2 2 0.425 1.008 + 3 ho 1 D2024 HO3 3 0.425 1.008 + 4 ho 1 D2024 HO4 4 0.425 1.008 + 5 oh 1 D2024 OH1 5 -0.95 16 + 6 oh 1 D2024 OH2 6 -0.95 16 + 7 oh 1 D2024 OH3 7 -0.95 16 + 8 oh 1 D2024 OH4 8 -0.95 16 + 9 ob 1 D2024 OB1 9 -1.05 16 + 10 obts 1 D2024 OBT2 10 -1.16875 16 ; Ob on Td Al + 11 ob 1 D2024 OB3 11 -1.05 16 + 12 ob 1 D2024 OB4 12 -1.05 16 + 13 ob 1 D2024 OB5 13 -1.05 16 + 14 ob 1 D2024 OB6 14 -1.05 16 + 15 ob 1 D2024 OB7 15 -1.05 16 + 16 ob 1 D2024 OB8 16 -1.05 16 + 17 obts 1 D2024 OBT9 17 -1.16875 16 ; Ob on Td Al + 18 obts 1 D2024 OBT10 18 -1.16875 16 ; Ob on Td Al + 19 obts 1 D2024 OBT11 19 -1.16875 16 ; Ob on Td Al + 20 ob 1 D2024 OB12 20 -1.05 16 + 21 ob 1 D2024 OB13 21 -1.05 16 + 22 ob 1 D2024 OB14 22 -1.05 16 + 23 ob 1 D2024 OB15 23 -1.05 16 + 24 ob 1 D2024 OB16 24 -1.05 16 + 25 ob 1 D2024 OB17 25 -1.05 16 + 26 ob 1 D2024 OB18 26 -1.05 16 + 27 ob 1 D2024 OB19 27 -1.05 16 + 28 ob 1 D2024 OB20 28 -1.05 16 + 29 ao 1 D2024 AO1 29 1.575 26.98 + 30 ao 1 D2024 AO2 30 1.575 26.98 + 31 ao 1 D2024 AO3 31 1.575 26.98 + 32 ao 1 D2024 AO4 32 1.575 26.98 + 33 st 1 D2024 ST1 33 2.1 28.09 + 34 at 1 D2024 AT2 34 1.575 26.98 ; subst to Td Al + 35 st 1 D2024 ST3 35 2.1 28.09 + 36 st 1 D2024 ST4 36 2.1 28.09 + 37 st 1 D2024 ST5 37 2.1 28.09 + 38 st 1 D2024 ST6 38 2.1 28.09 + 39 st 1 D2024 ST7 39 2.1 28.09 + 40 st 1 D2024 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2025.gro b/package/ClayCode/data/data/UCS/D21/D2025.gro new file mode 100644 index 00000000..12a064d1 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2025.gro @@ -0,0 +1,44 @@ +Smectite Unit Cell 1 x Td Al + 1 x Oct Mg +40 + 1D225 HO1 1 0.084 0.120 0.595 + 1D225 HO2 2 0.181 0.230 0.205 + 1D225 HO3 3 0.441 0.679 0.205 + 1D225 HO4 4 0.344 0.568 0.595 + 1D225 OH1 5 0.101 0.122 0.499 + 1D225 OH2 6 0.163 0.228 0.301 + 1D225 OHS3 7 0.424 0.677 0.301 + 1D225 OHS4 8 0.362 0.570 0.499 + 1D225 OBS1 9 0.317 0.847 0.506 + 1D225 OB2 10 0.361 0.225 0.507 + 1D225 OB3 11 0.463 0.400 0.294 + 1D225 OB4 12 0.419 0.125 0.294 + 1D225 OBS5 13 0.202 0.848 0.294 + 1D225 OBX6 14 0.164 0.574 0.294 + 1D225 OB7 15 0.062 0.399 0.506 + 1D225 OBS8 16 0.106 0.673 0.507 + 1D225 OB9 17 0.485 0.293 0.730 + 1D225 OB10 18 0.316 0.091 0.729 + 1D225 OB11 19 0.229 0.342 0.706 + 1D225 OB12 20 0.295 0.057 0.070 + 1D225 OB13 21 0.464 0.259 0.071 + 1D225 OB14 22 0.035 0.008 0.095 + 1D225 OBT15 23 0.040 0.505 0.070 + 1D225 OBT16 24 0.209 0.707 0.071 + 1D225 OBT17 25 0.296 0.457 0.095 + 1D225 OB18 26 0.229 0.742 0.730 + 1D225 OB19 27 0.061 0.539 0.729 + 1D225 OB20 28 0.490 0.790 0.706 + 1D225 AO1 29 0.260 0.101 0.400 + 1D225 AO2 30 0.004 0.249 0.400 + 1D225 MGO3 31 0.265 0.698 0.400 + 1D225 AO4 32 0.005 0.549 0.400 + 1D225 ST1 33 0.336 0.840 0.668 + 1D225 ST2 34 0.346 0.238 0.669 + 1D225 ST3 35 0.444 0.407 0.132 + 1D225 ST4 36 0.434 0.112 0.131 + 1D225 ST5 37 0.183 0.856 0.132 + 1D225 AT6 38 0.179 0.561 0.131 + 1D225 ST7 39 0.081 0.391 0.668 + 1D225 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + diff --git a/package/ClayCode/data/data/UCS/D21/D2025.itp b/package/ClayCode/data/data/UCS/D21/D2025.itp new file mode 100644 index 00000000..453d18d7 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2025.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2025 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2025rtp D2025 q -2.0 + 1 ho 1 D2025 HO1 1 0.425 1.008 + 2 ho 1 D2025 HO2 2 0.425 1.008 + 3 ho 1 D2025 HO3 3 0.425 1.008 + 4 ho 1 D2025 HO4 4 0.425 1.008 + 5 oh 1 D2025 OH1 5 -0.95 16 + 6 oh 1 D2025 OH2 6 -0.95 16 + 7 ohs 1 D2025 OHS3 7 -1.0808 16 ; OH on Mg + 8 ohs 1 D2025 OHS4 8 -1.0808 16 ; OH on Mg + 9 obos 1 D2025 OBS1 9 -1.1808 16 ; Ob on Mg + 10 ob 1 D2025 OB2 10 -1.05 16 + 11 ob 1 D2025 OB3 11 -1.05 16 + 12 ob 1 D2025 OB4 12 -1.05 16 + 13 obos 1 D2025 OBS5 13 -1.1808 16 ; Ob on Mg + 14 obss 1 D2025 OBX6 14 -1.29955 16 ; Ob on Mg and Td Al + 15 ob 1 D2025 OB7 15 -1.05 16 + 16 obos 1 D2025 OBS8 16 -1.1808 16 ; Ob on Mg + 17 ob 1 D2025 OB9 17 -1.05 16 + 18 ob 1 D2025 OB10 18 -1.05 16 + 19 ob 1 D2025 OB11 19 -1.05 16 + 20 ob 1 D2025 OB12 20 -1.05 16 + 21 ob 1 D2025 OB13 21 -1.05 16 + 22 ob 1 D2025 OB14 22 -1.05 16 + 23 obts 1 D2025 OBT15 23 -1.16875 16 + 24 obts 1 D2025 OBT16 24 -1.16875 16 + 25 obts 1 D2025 OBT17 25 -1.16875 16 + 26 ob 1 D2025 OB18 26 -1.05 16 + 27 ob 1 D2025 OB19 27 -1.05 16 + 28 ob 1 D2025 OB20 28 -1.05 16 + 29 ao 1 D2025 AO1 29 1.575 26.98 + 30 ao 1 D2025 AO2 30 1.575 26.98 + 31 mgo 1 D2025 MGO3 31 1.3598 24.31 ; subst Mg + 32 ao 1 D2025 AO4 32 1.575 26.98 + 33 st 1 D2025 ST1 33 2.1 28.09 + 34 st 1 D2025 ST2 34 2.1 28.09 + 35 st 1 D2025 ST3 35 2.1 28.09 + 36 st 1 D2025 ST4 36 2.1 28.09 + 37 st 1 D2025 ST5 37 2.1 28.09 + 38 at 1 D2025 AT6 38 1.575 26.98 ; subs Td Al + 39 st 1 D2025 ST7 39 2.1 28.09 + 40 st 1 D2025 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2026.gro b/package/ClayCode/data/data/UCS/D21/D2026.gro new file mode 100644 index 00000000..871b46d6 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2026.gro @@ -0,0 +1,45 @@ +Smectite Unit Cell 1 x Td Al + 1 x Oct Mg +40 + 1D226 HO1 1 0.084 0.120 0.595 + 1D226 HO2 2 0.181 0.230 0.205 + 1D226 HO3 3 0.441 0.679 0.205 + 1D226 HO4 4 0.344 0.568 0.595 + 1D226 OH1 5 0.101 0.122 0.499 + 1D226 OH2 6 0.163 0.228 0.301 + 1D226 OHS3 7 0.424 0.677 0.301 + 1D226 OHS4 8 0.362 0.570 0.499 + 1D226 OBS1 9 0.317 0.847 0.506 + 1D226 OBT2 10 0.361 0.225 0.507 + 1D226 OB3 11 0.463 0.400 0.294 + 1D226 OB4 12 0.419 0.125 0.294 + 1D226 OBS5 13 0.202 0.848 0.294 + 1D226 OBS6 14 0.164 0.574 0.294 + 1D226 OB7 15 0.062 0.399 0.506 + 1D226 OBS8 16 0.106 0.673 0.507 + 1D226 OBT9 17 0.485 0.293 0.730 + 1D226 OBT10 18 0.316 0.091 0.729 + 1D226 OBT11 19 0.229 0.342 0.706 + 1D226 OB12 20 0.295 0.057 0.070 + 1D226 OB13 21 0.464 0.259 0.071 + 1D226 OB14 22 0.035 0.008 0.095 + 1D226 OB15 23 0.040 0.505 0.070 + 1D226 OB16 24 0.209 0.707 0.071 + 1D226 OB17 25 0.296 0.457 0.095 + 1D226 OB18 26 0.229 0.742 0.730 + 1D226 OB19 27 0.061 0.539 0.729 + 1D226 OB20 28 0.490 0.790 0.706 + 1D226 AO1 29 0.260 0.101 0.400 + 1D226 AO2 30 0.004 0.249 0.400 + 1D226 MGO3 31 0.265 0.698 0.400 + 1D226 AO4 32 0.005 0.549 0.400 + 1D226 ST1 33 0.336 0.840 0.668 + 1D226 AT2 34 0.346 0.238 0.669 + 1D226 ST3 35 0.444 0.407 0.132 + 1D226 ST4 36 0.434 0.112 0.131 + 1D226 ST5 37 0.183 0.856 0.132 + 1D226 ST6 38 0.179 0.561 0.131 + 1D226 ST7 39 0.081 0.391 0.668 + 1D226 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + + diff --git a/package/ClayCode/data/data/UCS/D21/D2026.itp b/package/ClayCode/data/data/UCS/D21/D2026.itp new file mode 100644 index 00000000..0ce2f79b --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2026.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2026 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 UC3Trtp UC3T q -2.0 + 1 ho 1 D2026 HO1 1 0.425 1.008 + 2 ho 1 D2026 HO2 2 0.425 1.008 + 3 ho 1 D2026 HO3 3 0.425 1.008 + 4 ho 1 D2026 HO4 4 0.425 1.008 + 5 oh 1 D2026 OH1 5 -0.95 16 + 6 oh 1 D2026 OH2 6 -0.95 16 + 7 ohs 1 D2026 OHS3 7 -1.0808 16 ; OH on Mg + 8 ohs 1 D2026 OHS4 8 -1.0808 16 ; OH on Mg + 9 obos 1 D2026 OBS1 9 -1.1808 16 ; Ob on Mg + 10 obts 1 D2026 OBT2 10 -1.16875 16 ; Ob on Al + 11 ob 1 D2026 OB3 11 -1.05 16 + 12 ob 1 D2026 OB4 12 -1.05 16 + 13 obos 1 D2026 OBS5 13 -1.1808 16 ; Ob on Mg + 14 obos 1 D2026 OBS6 14 -1.1808 16 ; Ob on Mg + 15 ob 1 D2026 OB7 15 -1.05 16 + 16 obos 1 D2026 OBS8 16 -1.1808 16 ; Ob on Mg + 17 obts 1 D2026 OBT9 17 -1.16875 16 ; Ob on Al + 18 obts 1 D2026 OBT10 18 -1.16875 16 ; Ob on Al + 19 obts 1 D2026 OBT11 19 -1.16875 16 ; Ob on Al + 20 ob 1 D2026 OB12 20 -1.05 16 + 21 ob 1 D2026 OB13 21 -1.05 16 + 22 ob 1 D2026 OB14 22 -1.05 16 + 23 ob 1 D2026 OB15 23 -1.05 16 + 24 ob 1 D2026 OB16 24 -1.05 16 + 25 ob 1 D2026 OB17 25 -1.05 16 + 26 ob 1 D2026 OB18 26 -1.05 16 + 27 ob 1 D2026 OB19 27 -1.05 16 + 28 ob 1 D2026 OB20 28 -1.05 16 + 29 ao 1 D2026 AO1 29 1.575 26.98 + 30 ao 1 D2026 AO2 30 1.575 26.98 + 31 mgo 1 D2026 MGO3 31 1.3598 24.31 ; subst Mg + 32 ao 1 D2026 AO4 32 1.575 26.98 + 33 st 1 D2026 ST1 33 2.1 28.09 + 34 at 1 D2026 AT2 34 1.575 26.98 ; subs Td Al + 35 st 1 D2026 ST3 35 2.1 28.09 + 36 st 1 D2026 ST4 36 2.1 28.09 + 37 st 1 D2026 ST5 37 2.1 28.09 + 38 st 1 D2026 ST6 38 2.1 28.09 + 39 st 1 D2026 ST7 39 2.1 28.09 + 40 st 1 D2026 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2027.gro b/package/ClayCode/data/data/UCS/D21/D2027.gro new file mode 100644 index 00000000..a6a1eb8b --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2027.gro @@ -0,0 +1,43 @@ +Smectite Unit Cell 2 x Td Al +40 + 1D227 HO1 1 0.084 0.120 0.595 + 1D227 HO2 2 0.181 0.230 0.205 + 1D227 HO3 3 0.441 0.679 0.205 + 1D227 HO4 4 0.344 0.568 0.595 + 1D227 OH1 5 0.101 0.122 0.499 + 1D227 OH2 6 0.163 0.228 0.301 + 1D227 OH3 7 0.424 0.677 0.301 + 1D227 OH4 8 0.362 0.570 0.499 + 1D227 OB1 9 0.317 0.847 0.506 + 1D227 OBT2 10 0.361 0.225 0.507 + 1D227 OB3 11 0.463 0.400 0.294 + 1D227 OB4 12 0.419 0.125 0.294 + 1D227 OB5 13 0.202 0.848 0.294 + 1D227 OBT6 14 0.164 0.574 0.294 + 1D227 OB7 15 0.062 0.399 0.506 + 1D227 OB8 16 0.106 0.673 0.507 + 1D227 OBT9 17 0.485 0.293 0.730 + 1D227 OBT10 18 0.316 0.091 0.729 + 1D227 OBT11 19 0.229 0.342 0.706 + 1D227 OB12 20 0.295 0.057 0.070 + 1D227 OB13 21 0.464 0.259 0.071 + 1D227 OB14 22 0.035 0.008 0.095 + 1D227 OBT15 23 0.040 0.505 0.070 + 1D227 OBT16 24 0.209 0.707 0.071 + 1D227 OBT17 25 0.296 0.457 0.095 + 1D227 OB18 26 0.229 0.742 0.730 + 1D227 OB19 27 0.061 0.539 0.729 + 1D227 OB20 28 0.490 0.790 0.706 + 1D227 AO1 29 0.260 0.101 0.400 + 1D227 AO2 30 0.004 0.249 0.400 + 1D227 AO3 31 0.265 0.698 0.400 + 1D227 AO4 32 0.005 0.549 0.400 + 1D227 ST1 33 0.336 0.840 0.668 + 1D227 AT2 34 0.346 0.238 0.669 + 1D227 ST3 35 0.444 0.407 0.132 + 1D227 ST4 36 0.434 0.112 0.131 + 1D227 ST5 37 0.183 0.856 0.132 + 1D227 AT6 38 0.179 0.561 0.131 + 1D227 ST7 39 0.081 0.391 0.668 + 1D227 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 diff --git a/package/ClayCode/data/data/UCS/D21/D2027.itp b/package/ClayCode/data/data/UCS/D21/D2027.itp new file mode 100644 index 00000000..d5b73790 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2027.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2027 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2027rtp D2027 q -2.0 + 1 ho 1 D2027 HO1 1 0.425 1.008 + 2 ho 1 D2027 HO2 2 0.425 1.008 + 3 ho 1 D2027 HO3 3 0.425 1.008 + 4 ho 1 D2027 HO4 4 0.425 1.008 + 5 oh 1 D2027 OH1 5 -0.95 16 + 6 oh 1 D2027 OH2 6 -0.95 16 + 7 oh 1 D2027 OH3 7 -0.95 16 + 8 oh 1 D2027 OH4 8 -0.95 16 + 9 ob 1 D2027 OB1 9 -1.05 16 + 10 obts 1 D2027 OBT2 10 -1.16875 16 ; OB on Td Al + 11 ob 1 D2027 OB3 11 -1.05 16 + 12 ob 1 D2027 OB4 12 -1.05 16 + 13 ob 1 D2027 OB5 13 -1.05 16 + 14 obts 1 D2027 OBT6 14 -1.16875 16 ; OB on Td Al + 15 ob 1 D2027 OB7 15 -1.05 16 + 16 ob 1 D2027 OB8 16 -1.05 16 + 17 obts 1 D2027 OBT9 17 -1.16875 16 ; OB on Td Al + 18 obts 1 D2027 OBT10 18 -1.16875 16 ; OB on Td Al + 19 obts 1 D2027 OBT11 19 -1.16875 16 ; OB on Td Al + 20 ob 1 D2027 OB12 20 -1.05 16 + 21 ob 1 D2027 OB13 21 -1.05 16 + 22 ob 1 D2027 OB14 22 -1.05 16 + 23 obts 1 D2027 OBT15 23 -1.16875 16 ; OB on Td Al + 24 obts 1 D2027 OBT16 24 -1.16875 16 ; OB on Td Al + 25 obts 1 D2027 OBT17 25 -1.16875 16 ; OB on Td Al + 26 ob 1 D2027 OB18 26 -1.05 16 + 27 ob 1 D2027 OB19 27 -1.05 16 + 28 ob 1 D2027 OB20 28 -1.05 16 + 29 ao 1 D2027 AO1 29 1.575 26.98 + 30 ao 1 D2027 AO2 30 1.575 26.98 + 31 ao 1 D2027 AO3 31 1.575 26.98 + 32 ao 1 D2027 AO4 32 1.575 26.98 + 33 st 1 D2027 ST1 33 2.1 28.09 + 34 at 1 D2027 AT2 34 1.575 26.98 ; subs Td Al + 35 st 1 D2027 ST3 35 2.1 28.09 + 36 st 1 D2027 ST4 36 2.1 28.09 + 37 st 1 D2027 ST5 37 2.1 28.09 + 38 at 1 D2027 AT6 38 1.575 26.98 ; subs Td Al + 39 st 1 D2027 ST7 39 2.1 28.09 + 40 st 1 D2027 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2028.gro b/package/ClayCode/data/data/UCS/D21/D2028.gro new file mode 100644 index 00000000..f8082a9c --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2028.gro @@ -0,0 +1,43 @@ +Smectite Unit Cell 1 x Oct Fe3 +40 + 1D228 HO1 1 0.084 0.120 0.595 + 1D228 HO2 2 0.181 0.230 0.205 + 1D228 HO3 3 0.441 0.679 0.205 + 1D228 HO4 4 0.344 0.568 0.595 + 1D228 OH1 5 0.101 0.122 0.499 + 1D228 OH2 6 0.163 0.228 0.301 + 1D228 OH3 7 0.424 0.677 0.301 + 1D228 OH4 8 0.362 0.570 0.499 + 1D228 OB1 9 0.317 0.847 0.506 + 1D228 OB2 10 0.361 0.225 0.507 + 1D228 OB3 11 0.463 0.400 0.294 + 1D228 OB4 12 0.419 0.125 0.294 + 1D228 OB5 13 0.202 0.848 0.294 + 1D228 OB6 14 0.164 0.574 0.294 + 1D228 OB7 15 0.062 0.399 0.506 + 1D228 OB8 16 0.106 0.673 0.507 + 1D228 OB9 17 0.485 0.293 0.730 + 1D228 OB10 18 0.316 0.091 0.729 + 1D228 OB11 19 0.229 0.342 0.706 + 1D228 OB12 20 0.295 0.057 0.070 + 1D228 OB13 21 0.464 0.259 0.071 + 1D228 OB14 22 0.035 0.008 0.095 + 1D228 OB15 23 0.040 0.505 0.070 + 1D228 OB16 24 0.209 0.707 0.071 + 1D228 OB17 25 0.296 0.457 0.095 + 1D228 OB18 26 0.229 0.742 0.730 + 1D228 OB19 27 0.061 0.539 0.729 + 1D228 OB20 28 0.490 0.790 0.706 + 1D228 AO1 29 0.260 0.101 0.400 + 1D228 AO2 30 0.004 0.249 0.400 + 1D228 FO3 31 0.265 0.698 0.400 + 1D228 AO4 32 0.005 0.549 0.400 + 1D228 ST1 33 0.336 0.840 0.668 + 1D228 ST2 34 0.346 0.238 0.669 + 1D228 ST3 35 0.444 0.407 0.132 + 1D228 ST4 36 0.434 0.112 0.131 + 1D228 ST5 37 0.183 0.856 0.132 + 1D228 ST6 38 0.179 0.561 0.131 + 1D228 ST7 39 0.081 0.391 0.668 + 1D228 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 diff --git a/package/ClayCode/data/data/UCS/D21/D2028.itp b/package/ClayCode/data/data/UCS/D21/D2028.itp new file mode 100644 index 00000000..56a4492d --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2028.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2028 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 UC1 rtp UC1 q 0.0 + 1 ho 1 D2028 HO1 1 0.425 1.008 + 2 ho 1 D2028 HO2 2 0.425 1.008 + 3 ho 1 D2028 HO3 3 0.425 1.008 + 4 ho 1 D2028 HO4 4 0.425 1.008 + 5 oh 1 D2028 OH1 5 -0.95 16 + 6 oh 1 D2028 OH2 6 -0.95 16 + 7 oh 1 D2028 OH3 7 -0.95 16 + 8 oh 1 D2028 OH4 8 -0.95 16 + 9 ob 1 D2028 OB1 9 -1.05 16 + 10 ob 1 D2028 OB2 10 -1.05 16 + 11 ob 1 D2028 OB3 11 -1.05 16 + 12 ob 1 D2028 OB4 12 -1.05 16 + 13 ob 1 D2028 OB5 13 -1.05 16 + 14 ob 1 D2028 OB6 14 -1.05 16 + 15 ob 1 D2028 OB7 15 -1.05 16 + 16 ob 1 D2028 OB8 16 -1.05 16 + 17 ob 1 D2028 OB9 17 -1.05 16 + 18 ob 1 D2028 OB10 18 -1.05 16 + 19 ob 1 D2028 OB11 19 -1.05 16 + 20 ob 1 D2028 OB12 20 -1.05 16 + 21 ob 1 D2028 OB13 21 -1.05 16 + 22 ob 1 D2028 OB14 22 -1.05 16 + 23 ob 1 D2028 OB15 23 -1.05 16 + 24 ob 1 D2028 OB16 24 -1.05 16 + 25 ob 1 D2028 OB17 25 -1.05 16 + 26 ob 1 D2028 OB18 26 -1.05 16 + 27 ob 1 D2028 OB19 27 -1.05 16 + 28 ob 1 D2028 OB20 28 -1.05 16 + 29 ao 1 D2028 AO1 29 1.575 26.98 + 30 ao 1 D2028 AO2 30 1.575 26.98 + 31 feo 1 D2028 FO3 31 1.575 55.85 ; subst Fe III + 32 ao 1 D2028 AO4 32 1.575 26.98 + 33 st 1 D2028 ST1 33 2.1 28.09 + 34 st 1 D2028 ST2 34 2.1 28.09 + 35 st 1 D2028 ST3 35 2.1 28.09 + 36 st 1 D2028 ST4 36 2.1 28.09 + 37 st 1 D2028 ST5 37 2.1 28.09 + 38 st 1 D2028 ST6 38 2.1 28.09 + 39 st 1 D2028 ST7 39 2.1 28.09 + 40 st 1 D2028 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2029.gro b/package/ClayCode/data/data/UCS/D21/D2029.gro new file mode 100644 index 00000000..eb970a09 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2029.gro @@ -0,0 +1,43 @@ +Smectite Unit Cell 2 x Td Al + 1 x Oct Fe3 +40 + 1D229 HO1 1 0.084 0.120 0.595 + 1D229 HO2 2 0.181 0.230 0.205 + 1D229 HO3 3 0.441 0.679 0.205 + 1D229 HO4 4 0.344 0.568 0.595 + 1D229 OH1 5 0.101 0.122 0.499 + 1D229 OH2 6 0.163 0.228 0.301 + 1D229 OH3 7 0.424 0.677 0.301 + 1D229 OH4 8 0.362 0.570 0.499 + 1D229 OB1 9 0.317 0.847 0.506 + 1D229 OBT2 10 0.361 0.225 0.507 + 1D229 OB3 11 0.463 0.400 0.294 + 1D229 OB4 12 0.419 0.125 0.294 + 1D229 OB5 13 0.202 0.848 0.294 + 1D229 OBT6 14 0.164 0.574 0.294 + 1D229 OB7 15 0.062 0.399 0.506 + 1D229 OB8 16 0.106 0.673 0.507 + 1D229 OBT9 17 0.485 0.293 0.730 + 1D229 OBT10 18 0.316 0.091 0.729 + 1D229 OBT11 19 0.229 0.342 0.706 + 1D229 OB12 20 0.295 0.057 0.070 + 1D229 OB13 21 0.464 0.259 0.071 + 1D229 OB14 22 0.035 0.008 0.095 + 1D229 OBT15 23 0.040 0.505 0.070 + 1D229 OBT16 24 0.209 0.707 0.071 + 1D229 OBT17 25 0.296 0.457 0.095 + 1D229 OB18 26 0.229 0.742 0.730 + 1D229 OB19 27 0.061 0.539 0.729 + 1D229 OB20 28 0.490 0.790 0.706 + 1D229 AO1 29 0.260 0.101 0.400 + 1D229 AO2 30 0.004 0.249 0.400 + 1D229 FO3 31 0.265 0.698 0.400 + 1D229 AO4 32 0.005 0.549 0.400 + 1D229 ST1 33 0.336 0.840 0.668 + 1D229 AT2 34 0.346 0.238 0.669 + 1D229 ST3 35 0.444 0.407 0.132 + 1D229 ST4 36 0.434 0.112 0.131 + 1D229 ST5 37 0.183 0.856 0.132 + 1D229 AT6 38 0.179 0.561 0.131 + 1D229 ST7 39 0.081 0.391 0.668 + 1D229 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 diff --git a/package/ClayCode/data/data/UCS/D21/D2029.itp b/package/ClayCode/data/data/UCS/D21/D2029.itp new file mode 100644 index 00000000..d10077f9 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2029.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2029 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2029rtp D2029 q -2.0 + 1 ho 1 D2029 HO1 1 0.425 1.008 + 2 ho 1 D2029 HO2 2 0.425 1.008 + 3 ho 1 D2029 HO3 3 0.425 1.008 + 4 ho 1 D2029 HO4 4 0.425 1.008 + 5 oh 1 D2029 OH1 5 -0.95 16 + 6 oh 1 D2029 OH2 6 -0.95 16 + 7 oh 1 D2029 OH3 7 -0.95 16 + 8 oh 1 D2029 OH4 8 -0.95 16 + 9 ob 1 D2029 OB1 9 -1.05 16 + 10 obts 1 D2029 OBT2 10 -1.16875 16 ; OB on Td Al + 11 ob 1 D2029 OB3 11 -1.05 16 + 12 ob 1 D2029 OB4 12 -1.05 16 + 13 ob 1 D2029 OB5 13 -1.05 16 + 14 obts 1 D2029 OBT6 14 -1.16875 16 ; OB on Td Al + 15 ob 1 D2029 OB7 15 -1.05 16 + 16 ob 1 D2029 OB8 16 -1.05 16 + 17 obts 1 D2029 OBT9 17 -1.16875 16 ; OB on Td Al + 18 obts 1 D2029 OBT10 18 -1.16875 16 ; OB on Td Al + 19 obts 1 D2029 OBT11 19 -1.16875 16 ; OB on Td Al + 20 ob 1 D2029 OB12 20 -1.05 16 + 21 ob 1 D2029 OB13 21 -1.05 16 + 22 ob 1 D2029 OB14 22 -1.05 16 + 23 obts 1 D2029 OBT15 23 -1.16875 16 ; OB on Td Al + 24 obts 1 D2029 OBT16 24 -1.16875 16 ; OB on Td Al + 25 obts 1 D2029 OBT17 25 -1.16875 16 ; OB on Td Al + 26 ob 1 D2029 OB18 26 -1.05 16 + 27 ob 1 D2029 OB19 27 -1.05 16 + 28 ob 1 D2029 OB20 28 -1.05 16 + 29 ao 1 D2029 AO1 29 1.575 26.98 + 30 ao 1 D2029 AO2 30 1.575 26.98 + 31 feo 1 D2029 FO3 31 1.575 55.85 ; subst Fe III + 32 ao 1 D2029 AO4 32 1.575 26.98 + 33 st 1 D2029 ST1 33 2.1 28.09 + 34 at 1 D2029 AT2 34 1.575 26.98 ; subs Td Al + 35 st 1 D2029 ST3 35 2.1 28.09 + 36 st 1 D2029 ST4 36 2.1 28.09 + 37 st 1 D2029 ST5 37 2.1 28.09 + 38 at 1 D2029 AT6 38 1.575 26.98 ; subs Td Al + 39 st 1 D2029 ST7 39 2.1 28.09 + 40 st 1 D2029 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2030.gro b/package/ClayCode/data/data/UCS/D21/D2030.gro new file mode 100644 index 00000000..81aeda75 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2030.gro @@ -0,0 +1,44 @@ +Smectite Unit Cell 1 x Td Al + 1 x Oct Fe3 +40 + 1D230 HO1 1 0.084 0.120 0.595 + 1D230 HO2 2 0.181 0.230 0.205 + 1D230 HO3 3 0.441 0.679 0.205 + 1D230 HO4 4 0.344 0.568 0.595 + 1D230 OH1 5 0.101 0.122 0.499 + 1D230 OH2 6 0.163 0.228 0.301 + 1D230 OH3 7 0.424 0.677 0.301 + 1D230 OH4 8 0.362 0.570 0.499 + 1D230 OB1 9 0.317 0.847 0.506 + 1D230 OB2 10 0.361 0.225 0.507 + 1D230 OB3 11 0.463 0.400 0.294 + 1D230 OB4 12 0.419 0.125 0.294 + 1D230 OB5 13 0.202 0.848 0.294 + 1D230 OBT6 14 0.164 0.574 0.294 + 1D230 OB7 15 0.062 0.399 0.506 + 1D230 OB8 16 0.106 0.673 0.507 + 1D230 OB9 17 0.485 0.293 0.730 + 1D230 OB10 18 0.316 0.091 0.729 + 1D230 OB11 19 0.229 0.342 0.706 + 1D230 OB12 20 0.295 0.057 0.070 + 1D230 OB13 21 0.464 0.259 0.071 + 1D230 OB14 22 0.035 0.008 0.095 + 1D230 OBT15 23 0.040 0.505 0.070 + 1D230 OBT16 24 0.209 0.707 0.071 + 1D230 OBT17 25 0.296 0.457 0.095 + 1D230 OB18 26 0.229 0.742 0.730 + 1D230 OB19 27 0.061 0.539 0.729 + 1D230 OB20 28 0.490 0.790 0.706 + 1D230 FO1 29 0.260 0.101 0.400 + 1D230 AO2 30 0.004 0.249 0.400 + 1D230 AO3 31 0.265 0.698 0.400 + 1D230 AO4 32 0.005 0.549 0.400 + 1D230 ST1 33 0.336 0.840 0.668 + 1D230 ST2 34 0.346 0.238 0.669 + 1D230 ST3 35 0.444 0.407 0.132 + 1D230 ST4 36 0.434 0.112 0.131 + 1D230 ST5 37 0.183 0.856 0.132 + 1D230 AT6 38 0.179 0.561 0.131 + 1D230 ST7 39 0.081 0.391 0.668 + 1D230 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + diff --git a/package/ClayCode/data/data/UCS/D21/D2030.itp b/package/ClayCode/data/data/UCS/D21/D2030.itp new file mode 100644 index 00000000..4d08aafd --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2030.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2030 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2030rtp D2030 q -1.0 + 1 ho 1 D2030 HO1 1 0.425 1.008 + 2 ho 1 D2030 HO2 2 0.425 1.008 + 3 ho 1 D2030 HO3 3 0.425 1.008 + 4 ho 1 D2030 HO4 4 0.425 1.008 + 5 oh 1 D2030 OH1 5 -0.95 16 + 6 oh 1 D2030 OH2 6 -0.95 16 + 7 oh 1 D2030 OH3 7 -0.95 16 + 8 oh 1 D2030 OH4 8 -0.95 16 + 9 ob 1 D2030 OB1 9 -1.05 16 + 10 ob 1 D2030 OB2 10 -1.05 16 + 11 ob 1 D2030 OB3 11 -1.05 16 + 12 ob 1 D2030 OB4 12 -1.05 16 + 13 ob 1 D2030 OB5 13 -1.05 16 + 14 obts 1 D2030 OBT6 14 -1.16875 16 ; Ob on Td Al + 15 ob 1 D2030 OB7 15 -1.05 16 + 16 ob 1 D2030 OB8 16 -1.05 16 + 17 ob 1 D2030 OB9 17 -1.05 16 + 18 ob 1 D2030 OB10 18 -1.05 16 + 19 ob 1 D2030 OB11 19 -1.05 16 + 20 ob 1 D2030 OB12 20 -1.05 16 + 21 ob 1 D2030 OB13 21 -1.05 16 + 22 ob 1 D2030 OB14 22 -1.05 16 + 23 obts 1 D2030 OBT15 23 -1.16875 16 ; Ob on Td Al + 24 obts 1 D2030 OBT16 24 -1.16875 16 ; Ob on Td Al + 25 obts 1 D2030 OBT17 25 -1.16875 16 ; Ob on Td Al + 26 ob 1 D2030 OB18 26 -1.05 16 + 27 ob 1 D2030 OB19 27 -1.05 16 + 28 ob 1 D2030 OB20 28 -1.05 16 + 29 feo 1 D2030 FO1 29 1.575 55.85 ; subst Fe III + 30 ao 1 D2030 AO2 30 1.575 26.98 + 31 ao 1 D2030 AO3 31 1.575 26.98 + 32 ao 1 D2030 AO4 32 1.575 26.98 + 33 st 1 D2030 ST1 33 2.1 28.09 + 34 st 1 D2030 ST2 34 2.1 28.09 + 35 st 1 D2030 ST3 35 2.1 28.09 + 36 st 1 D2030 ST4 36 2.1 28.09 + 37 st 1 D2030 ST5 37 2.1 28.09 + 38 at 1 D2030 AT6 38 1.575 26.98 ; subst to Td Al + 39 st 1 D2030 ST7 39 2.1 28.09 + 40 st 1 D2030 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2031.gro b/package/ClayCode/data/data/UCS/D21/D2031.gro new file mode 100644 index 00000000..c23c2c4e --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2031.gro @@ -0,0 +1,44 @@ +Smectite Unit Cell 1 x Td Al + 1 x Oct Fe3 +40 + 1D231 HO1 1 0.084 0.120 0.595 + 1D231 HO2 2 0.181 0.230 0.205 + 1D231 HO3 3 0.441 0.679 0.205 + 1D231 HO4 4 0.344 0.568 0.595 + 1D231 OH1 5 0.101 0.122 0.499 + 1D231 OH2 6 0.163 0.228 0.301 + 1D231 OH3 7 0.424 0.677 0.301 + 1D231 OH4 8 0.362 0.570 0.499 + 1D231 OB1 9 0.317 0.847 0.506 + 1D231 OBT2 10 0.361 0.225 0.507 + 1D231 OB3 11 0.463 0.400 0.294 + 1D231 OB4 12 0.419 0.125 0.294 + 1D231 OB5 13 0.202 0.848 0.294 + 1D231 OB6 14 0.164 0.574 0.294 + 1D231 OB7 15 0.062 0.399 0.506 + 1D231 OB8 16 0.106 0.673 0.507 + 1D231 OBT9 17 0.485 0.293 0.730 + 1D231 OBT10 18 0.316 0.091 0.729 + 1D231 OBT11 19 0.229 0.342 0.706 + 1D231 OB12 20 0.295 0.057 0.070 + 1D231 OB13 21 0.464 0.259 0.071 + 1D231 OB14 22 0.035 0.008 0.095 + 1D231 OB15 23 0.040 0.505 0.070 + 1D231 OB16 24 0.209 0.707 0.071 + 1D231 OB17 25 0.296 0.457 0.095 + 1D231 OB18 26 0.229 0.742 0.730 + 1D231 OB19 27 0.061 0.539 0.729 + 1D231 OB20 28 0.490 0.790 0.706 + 1D231 AO1 29 0.260 0.101 0.400 + 1D231 AO2 30 0.004 0.249 0.400 + 1D231 AO3 31 0.265 0.698 0.400 + 1D231 FO4 32 0.005 0.549 0.400 + 1D231 ST1 33 0.336 0.840 0.668 + 1D231 AT2 34 0.346 0.238 0.669 + 1D231 ST3 35 0.444 0.407 0.132 + 1D231 ST4 36 0.434 0.112 0.131 + 1D231 ST5 37 0.183 0.856 0.132 + 1D231 ST6 38 0.179 0.561 0.131 + 1D231 ST7 39 0.081 0.391 0.668 + 1D231 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 + diff --git a/package/ClayCode/data/data/UCS/D21/D2031.itp b/package/ClayCode/data/data/UCS/D21/D2031.itp new file mode 100644 index 00000000..4666700a --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2031.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2031 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2031rtp D2031 q -1.0 + 1 ho 1 D2031 HO1 1 0.425 1.008 + 2 ho 1 D2031 HO2 2 0.425 1.008 + 3 ho 1 D2031 HO3 3 0.425 1.008 + 4 ho 1 D2031 HO4 4 0.425 1.008 + 5 oh 1 D2031 OH1 5 -0.95 16 + 6 oh 1 D2031 OH2 6 -0.95 16 + 7 oh 1 D2031 OH3 7 -0.95 16 + 8 oh 1 D2031 OH4 8 -0.95 16 + 9 ob 1 D2031 OB1 9 -1.05 16 + 10 obts 1 D2031 OBT2 10 -1.16875 16 ; Ob on Td Al + 11 ob 1 D2031 OB3 11 -1.05 16 + 12 ob 1 D2031 OB4 12 -1.05 16 + 13 ob 1 D2031 OB5 13 -1.05 16 + 14 ob 1 D2031 OB6 14 -1.05 16 + 15 ob 1 D2031 OB7 15 -1.05 16 + 16 ob 1 D2031 OB8 16 -1.05 16 + 17 obts 1 D2031 OBT9 17 -1.16875 16 ; Ob on Td Al + 18 obts 1 D2031 OBT10 18 -1.16875 16 ; Ob on Td Al + 19 obts 1 D2031 OBT11 19 -1.16875 16 ; Ob on Td Al + 20 ob 1 D2031 OB12 20 -1.05 16 + 21 ob 1 D2031 OB13 21 -1.05 16 + 22 ob 1 D2031 OB14 22 -1.05 16 + 23 ob 1 D2031 OB15 23 -1.05 16 + 24 ob 1 D2031 OB16 24 -1.05 16 + 25 ob 1 D2031 OB17 25 -1.05 16 + 26 ob 1 D2031 OB18 26 -1.05 16 + 27 ob 1 D2031 OB19 27 -1.05 16 + 28 ob 1 D2031 OB20 28 -1.05 16 + 29 ao 1 D2031 AO1 29 1.575 26.98 + 30 ao 1 D2031 AO2 30 1.575 26.98 + 31 ao 1 D2031 AO3 31 1.575 26.98 + 32 feo 1 D2031 FO4 32 1.575 55.85 ; subst Fe III + 33 st 1 D2031 ST1 33 2.1 28.09 + 34 at 1 D2031 AT2 34 1.575 26.98 ; subst to Td Al + 35 st 1 D2031 ST3 35 2.1 28.09 + 36 st 1 D2031 ST4 36 2.1 28.09 + 37 st 1 D2031 ST5 37 2.1 28.09 + 38 st 1 D2031 ST6 38 2.1 28.09 + 39 st 1 D2031 ST7 39 2.1 28.09 + 40 st 1 D2031 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2036.gro b/package/ClayCode/data/data/UCS/D21/D2036.gro new file mode 100644 index 00000000..cd122983 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2036.gro @@ -0,0 +1,43 @@ +Smectite Unit Cell 1 x Oct Fe2 +40 + 1D236 HO1 1 0.084 0.120 0.595 + 1D236 HO2 2 0.181 0.230 0.205 + 1D236 HO3 3 0.441 0.679 0.205 + 1D236 HO4 4 0.344 0.568 0.595 + 1D236 OH1 5 0.101 0.122 0.499 + 1D236 OH2 6 0.163 0.228 0.301 + 1D236 OHS3 7 0.424 0.677 0.301 + 1D236 OHS4 8 0.362 0.570 0.499 + 1D236 OBS1 9 0.317 0.847 0.506 + 1D236 OB2 10 0.361 0.225 0.507 + 1D236 OB3 11 0.463 0.400 0.294 + 1D236 OB4 12 0.419 0.125 0.294 + 1D236 OBS5 13 0.202 0.848 0.294 + 1D236 OBS6 14 0.164 0.574 0.294 + 1D236 OB7 15 0.062 0.399 0.506 + 1D236 OBS8 16 0.106 0.673 0.507 + 1D236 OB9 17 0.485 0.293 0.730 + 1D236 OB10 18 0.316 0.091 0.729 + 1D236 OB11 19 0.229 0.342 0.706 + 1D236 OB12 20 0.295 0.057 0.070 + 1D236 OB13 21 0.464 0.259 0.071 + 1D236 OB14 22 0.035 0.008 0.095 + 1D236 OB15 23 0.040 0.505 0.070 + 1D236 OB16 24 0.209 0.707 0.071 + 1D236 OB17 25 0.296 0.457 0.095 + 1D236 OB18 26 0.229 0.742 0.730 + 1D236 OB19 27 0.061 0.539 0.729 + 1D236 OB20 28 0.490 0.790 0.706 + 1D236 AO1 29 0.260 0.101 0.400 + 1D236 AO2 30 0.004 0.249 0.400 + 1D236 FE23 31 0.265 0.698 0.400 + 1D236 AO4 32 0.005 0.549 0.400 + 1D236 ST1 33 0.336 0.840 0.668 + 1D236 ST2 34 0.346 0.238 0.669 + 1D236 ST3 35 0.444 0.407 0.132 + 1D236 ST4 36 0.434 0.112 0.131 + 1D236 ST5 37 0.183 0.856 0.132 + 1D236 ST6 38 0.179 0.561 0.131 + 1D236 ST7 39 0.081 0.391 0.668 + 1D236 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 diff --git a/package/ClayCode/data/data/UCS/D21/D2036.itp b/package/ClayCode/data/data/UCS/D21/D2036.itp new file mode 100644 index 00000000..871e6129 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2036.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2036 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2036rtp D2036 q -1 + 1 ho 1 D2036 HO1 1 0.425 1.008 + 2 ho 1 D2036 HO2 2 0.425 1.008 + 3 ho 1 D2036 HO3 3 0.425 1.008 + 4 ho 1 D2036 HO4 4 0.425 1.008 + 5 oh 1 D2036 OH1 5 -0.95 16 + 6 oh 1 D2036 OH2 6 -0.95 16 + 7 ohs 1 D2036 OHS3 7 -1.0808 16 ; OH on Fe2 + 8 ohs 1 D2036 OHS4 8 -1.0808 16 ; OH on Fe2 + 9 obos 1 D2036 OBS1 9 -1.1808 16 ; Ob on Fe2 + 10 ob 1 D2036 OB2 10 -1.05 16 + 11 ob 1 D2036 OB3 11 -1.05 16 + 12 ob 1 D2036 OB4 12 -1.05 16 + 13 obos 1 D2036 OBS5 13 -1.1808 16 ; Ob on Fe2 + 14 obos 1 D2036 OBS6 14 -1.1808 16 ; Ob on Fe2 + 15 ob 1 D2036 OB7 15 -1.05 16 + 16 obos 1 D2036 OBS8 16 -1.1808 16 ; Ob on Fe2 + 17 ob 1 D2036 OB9 17 -1.05 16 + 18 ob 1 D2036 OB10 18 -1.05 16 + 19 ob 1 D2036 OB11 19 -1.05 16 + 20 ob 1 D2036 OB12 20 -1.05 16 + 21 ob 1 D2036 OB13 21 -1.05 16 + 22 ob 1 D2036 OB14 22 -1.05 16 + 23 ob 1 D2036 OB15 23 -1.05 16 + 24 ob 1 D2036 OB16 24 -1.05 16 + 25 ob 1 D2036 OB17 25 -1.05 16 + 26 ob 1 D2036 OB18 26 -1.05 16 + 27 ob 1 D2036 OB19 27 -1.05 16 + 28 ob 1 D2036 OB20 28 -1.05 16 + 29 ao 1 D2036 AO1 29 1.575 26.98 + 30 ao 1 D2036 AO2 30 1.575 26.98 + 31 fe2 1 D2036 FE23 31 1.3598 55.85 ; subst Fe2 + 32 ao 1 D2036 AO4 32 1.575 26.98 + 33 st 1 D2036 ST1 33 2.1 28.09 + 34 st 1 D2036 ST2 34 2.1 28.09 + 35 st 1 D2036 ST3 35 2.1 28.09 + 36 st 1 D2036 ST4 36 2.1 28.09 + 37 st 1 D2036 ST5 37 2.1 28.09 + 38 st 1 D2036 ST6 38 2.1 28.09 + 39 st 1 D2036 ST7 39 2.1 28.09 + 40 st 1 D2036 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2037.gro b/package/ClayCode/data/data/UCS/D21/D2037.gro new file mode 100644 index 00000000..7b59c126 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2037.gro @@ -0,0 +1,43 @@ +Smectite Unit Cell 1 x Oct Fe2 + 1 x Td Al +40 + 1D237 HO1 1 0.084 0.120 0.595 + 1D237 HO2 2 0.181 0.230 0.205 + 1D237 HO3 3 0.441 0.679 0.205 + 1D237 HO4 4 0.344 0.568 0.595 + 1D237 OH1 5 0.101 0.122 0.499 + 1D237 OH2 6 0.163 0.228 0.301 + 1D237 OHS3 7 0.424 0.677 0.301 + 1D237 OHS4 8 0.362 0.570 0.499 + 1D237 OBS1 9 0.317 0.847 0.506 + 1D237 OB2 10 0.361 0.225 0.507 + 1D237 OB3 11 0.463 0.400 0.294 + 1D237 OB4 12 0.419 0.125 0.294 + 1D237 OBS5 13 0.202 0.848 0.294 + 1D237 OBX6 14 0.164 0.574 0.294 + 1D237 OB7 15 0.062 0.399 0.506 + 1D237 OBS8 16 0.106 0.673 0.507 + 1D237 OB9 17 0.485 0.293 0.730 + 1D237 OB10 18 0.316 0.091 0.729 + 1D237 OB11 19 0.229 0.342 0.706 + 1D237 OB12 20 0.295 0.057 0.070 + 1D237 OB13 21 0.464 0.259 0.071 + 1D237 OB14 22 0.035 0.008 0.095 + 1D237 OBT15 23 0.040 0.505 0.070 + 1D237 OBT16 24 0.209 0.707 0.071 + 1D237 OBT17 25 0.296 0.457 0.095 + 1D237 OB18 26 0.229 0.742 0.730 + 1D237 OB19 27 0.061 0.539 0.729 + 1D237 OB20 28 0.490 0.790 0.706 + 1D237 AO1 29 0.260 0.101 0.400 + 1D237 AO2 30 0.004 0.249 0.400 + 1D237 FE23 31 0.265 0.698 0.400 + 1D237 AO4 32 0.005 0.549 0.400 + 1D237 ST1 33 0.336 0.840 0.668 + 1D237 ST2 34 0.346 0.238 0.669 + 1D237 ST3 35 0.444 0.407 0.132 + 1D237 ST4 36 0.434 0.112 0.131 + 1D237 ST5 37 0.183 0.856 0.132 + 1D237 AT6 38 0.179 0.561 0.131 + 1D237 ST7 39 0.081 0.391 0.668 + 1D237 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 diff --git a/package/ClayCode/data/data/UCS/D21/D2037.itp b/package/ClayCode/data/data/UCS/D21/D2037.itp new file mode 100644 index 00000000..47fa570d --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2037.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2037 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 D2037rtp D2037 q -2.0 + 1 ho 1 D2037 HO1 1 0.425 1.008 + 2 ho 1 D2037 HO2 2 0.425 1.008 + 3 ho 1 D2037 HO3 3 0.425 1.008 + 4 ho 1 D2037 HO4 4 0.425 1.008 + 5 oh 1 D2037 OH1 5 -0.95 16 + 6 oh 1 D2037 OH2 6 -0.95 16 + 7 ohs 1 D2037 OHS3 7 -1.0808 16 ; OH on Fe2 + 8 ohs 1 D2037 OHS4 8 -1.0808 16 ; OH on Fe2 + 9 obos 1 D2037 OBS1 9 -1.1808 16 ; Ob on Fe2 + 10 ob 1 D2037 OB2 10 -1.05 16 + 11 ob 1 D2037 OB3 11 -1.05 16 + 12 ob 1 D2037 OB4 12 -1.05 16 + 13 obos 1 D2037 OBS5 13 -1.1808 16 ; Ob on Fe2 + 14 obss 1 D2037 OBX6 14 -1.29955 16 ; Ob on Fe2 and Td Al + 15 ob 1 D2037 OB7 15 -1.05 16 + 16 obos 1 D2037 OBS8 16 -1.1808 16 ; Ob on Fe2 + 17 ob 1 D2037 OB9 17 -1.05 16 + 18 ob 1 D2037 OB10 18 -1.05 16 + 19 ob 1 D2037 OB11 19 -1.05 16 + 20 ob 1 D2037 OB12 20 -1.05 16 + 21 ob 1 D2037 OB13 21 -1.05 16 + 22 ob 1 D2037 OB14 22 -1.05 16 + 23 obts 1 D2037 OBT15 23 -1.16875 16 + 24 obts 1 D2037 OBT16 24 -1.16875 16 + 25 obts 1 D2037 OBT17 25 -1.16875 16 + 26 ob 1 D2037 OB18 26 -1.05 16 + 27 ob 1 D2037 OB19 27 -1.05 16 + 28 ob 1 D2037 OB20 28 -1.05 16 + 29 ao 1 D2037 AO1 29 1.575 26.98 + 30 ao 1 D2037 AO2 30 1.575 26.98 + 31 fe2 1 D2037 FE23 31 1.3598 55.85 ; subst Fe2 + 32 ao 1 D2037 AO4 32 1.575 26.98 + 33 st 1 D2037 ST1 33 2.1 28.09 + 34 st 1 D2037 ST2 34 2.1 28.09 + 35 st 1 D2037 ST3 35 2.1 28.09 + 36 st 1 D2037 ST4 36 2.1 28.09 + 37 st 1 D2037 ST5 37 2.1 28.09 + 38 at 1 D2037 AT6 38 1.575 26.98 ; subs Td Al + 39 st 1 D2037 ST7 39 2.1 28.09 + 40 st 1 D2037 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808 diff --git a/package/ClayCode/data/data/UCS/D21/D2038.gro b/package/ClayCode/data/data/UCS/D21/D2038.gro new file mode 100644 index 00000000..7ae87e68 --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2038.gro @@ -0,0 +1,43 @@ +Smectite Unit Cell 1 x Oct Fe2 + 1 x Td Al +40 + 1D238 HO1 1 0.084 0.120 0.595 + 1D238 HO2 2 0.181 0.230 0.205 + 1D238 HO3 3 0.441 0.679 0.205 + 1D238 HO4 4 0.344 0.568 0.595 + 1D238 OH1 5 0.101 0.122 0.499 + 1D238 OH2 6 0.163 0.228 0.301 + 1D238 OHS3 7 0.424 0.677 0.301 + 1D238 OHS4 8 0.362 0.570 0.499 + 1D238 OBS1 9 0.317 0.847 0.506 + 1D238 OBT2 10 0.361 0.225 0.507 + 1D238 OB3 11 0.463 0.400 0.294 + 1D238 OB4 12 0.419 0.125 0.294 + 1D238 OBS5 13 0.202 0.848 0.294 + 1D238 OBS6 14 0.164 0.574 0.294 + 1D238 OB7 15 0.062 0.399 0.506 + 1D238 OBS8 16 0.106 0.673 0.507 + 1D238 OBT9 17 0.485 0.293 0.730 + 1D238 OBT10 18 0.316 0.091 0.729 + 1D238 OBT11 19 0.229 0.342 0.706 + 1D238 OB12 20 0.295 0.057 0.070 + 1D238 OB13 21 0.464 0.259 0.071 + 1D238 OB14 22 0.035 0.008 0.095 + 1D238 OB15 23 0.040 0.505 0.070 + 1D238 OB16 24 0.209 0.707 0.071 + 1D238 OB17 25 0.296 0.457 0.095 + 1D238 OB18 26 0.229 0.742 0.730 + 1D238 OB19 27 0.061 0.539 0.729 + 1D238 OB20 28 0.490 0.790 0.706 + 1D238 AO1 29 0.260 0.101 0.400 + 1D238 AO2 30 0.004 0.249 0.400 + 1D238 FE23 31 0.265 0.698 0.400 + 1D238 AO4 32 0.005 0.549 0.400 + 1D238 ST1 33 0.336 0.840 0.668 + 1D238 AT2 34 0.346 0.238 0.669 + 1D238 ST3 35 0.444 0.407 0.132 + 1D238 ST4 36 0.434 0.112 0.131 + 1D238 ST5 37 0.183 0.856 0.132 + 1D238 ST6 38 0.179 0.561 0.131 + 1D238 ST7 39 0.081 0.391 0.668 + 1D238 ST8 40 0.091 0.686 0.669 + 0.5160 0.8966 0.9347 diff --git a/package/ClayCode/data/data/UCS/D21/D2038.itp b/package/ClayCode/data/data/UCS/D21/D2038.itp new file mode 100644 index 00000000..b476cb0e --- /dev/null +++ b/package/ClayCode/data/data/UCS/D21/D2038.itp @@ -0,0 +1,57 @@ +; +; +[ moleculetype ] +; name nrexcl + D2038 1 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 UC3Trtp UC3T q -2.0 + 1 ho 1 D2038 HO1 1 0.425 1.008 + 2 ho 1 D2038 HO2 2 0.425 1.008 + 3 ho 1 D2038 HO3 3 0.425 1.008 + 4 ho 1 D2038 HO4 4 0.425 1.008 + 5 oh 1 D2038 OH1 5 -0.95 16 + 6 oh 1 D2038 OH2 6 -0.95 16 + 7 ohs 1 D2038 OHS3 7 -1.0808 16 ; OH on Fe2 + 8 ohs 1 D2038 OHS4 8 -1.0808 16 ; OH on Fe2 + 9 obos 1 D2038 OBS1 9 -1.1808 16 ; Ob on Fe2 + 10 obts 1 D2038 OBT2 10 -1.16875 16 ; Ob on Al + 11 ob 1 D2038 OB3 11 -1.05 16 + 12 ob 1 D2038 OB4 12 -1.05 16 + 13 obos 1 D2038 OBS5 13 -1.1808 16 ; Ob on Fe2 + 14 obos 1 D2038 OBS6 14 -1.1808 16 ; Ob on Fe2 + 15 ob 1 D2038 OB7 15 -1.05 16 + 16 obos 1 D2038 OBS8 16 -1.1808 16 ; Ob on Fe2 + 17 obts 1 D2038 OBT9 17 -1.16875 16 ; Ob on Al + 18 obts 1 D2038 OBT10 18 -1.16875 16 ; Ob on Al + 19 obts 1 D2038 OBT11 19 -1.16875 16 ; Ob on Al + 20 ob 1 D2038 OB12 20 -1.05 16 + 21 ob 1 D2038 OB13 21 -1.05 16 + 22 ob 1 D2038 OB14 22 -1.05 16 + 23 ob 1 D2038 OB15 23 -1.05 16 + 24 ob 1 D2038 OB16 24 -1.05 16 + 25 ob 1 D2038 OB17 25 -1.05 16 + 26 ob 1 D2038 OB18 26 -1.05 16 + 27 ob 1 D2038 OB19 27 -1.05 16 + 28 ob 1 D2038 OB20 28 -1.05 16 + 29 ao 1 D2038 AO1 29 1.575 26.98 + 30 ao 1 D2038 AO2 30 1.575 26.98 + 31 fe2 1 D2038 FE23 31 1.3598 55.85 ; subst Fe2 + 32 ao 1 D2038 AO4 32 1.575 26.98 + 33 st 1 D2038 ST1 33 2.1 28.09 + 34 at 1 D2038 AT2 34 1.575 26.98 ; subs Td Al + 35 st 1 D2038 ST3 35 2.1 28.09 + 36 st 1 D2038 ST4 36 2.1 28.09 + 37 st 1 D2038 ST5 37 2.1 28.09 + 38 st 1 D2038 ST6 38 2.1 28.09 + 39 st 1 D2038 ST7 39 2.1 28.09 + 40 st 1 D2038 ST8 40 2.1 28.09 + + +[ bonds ] +; i j funct length force.c. +1 5 1 0.1 463532.808 +2 6 1 0.1 463532.808 +3 7 1 0.1 463532.808 +4 8 1 0.1 463532.808