mdkits 0.1.29__py3-none-any.whl → 0.1.30__py3-none-any.whl

mdkits/build_cli/adsorbate.py

@@ -18,6 +18,7 @@ from mdkits.util import arg_type, encapsulated_ase, out_err
 @click.option('--offset', type=click.Tuple([float, float]), help='adjust site', default=(0, 0), show_default=True)
 @click.option("--cover", type=int, help='cover the surface with adsorbate randomly')
 def main(atoms, adsorbate, cell, select, height, rotate, offset, cover):
+    """add adsorbate molcule to the surface"""
     if height is None:
         raise ValueError("height is required")
 

mdkits/build_cli/build_surface.py

@@ -22,10 +22,7 @@ def surface_check(obj, surface_type):
 @click.option('--orth', is_flag=True, help='if specified and true, forces the creation of a unit cell with orthogonal basis vectors. if the default is such a unit cell, this argument is not supported')
 @click.option('--vacuum', type=float, help='designate vacuum of surface, default is None', default=0.1, show_default=True)
 def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum):
-    #if args.primitive:
-    #    a = args.a * 0.7071 * 2
-    #else:
-    #    a = args.a
+    """build a common surface"""
 
     vacuum = vacuum / 2
     build_surface = surface_check(build, surface)

mdkits/md_cli/angle.py

@@ -5,6 +5,7 @@ import MDAnalysis
 import sys
 from mdkits.util import numpy_geo, encapsulated_mda, arg_type
 import numpy as np
+from .setting import common_setting
 
 
 class Angle_distribution(AnalysisBase):
@@ -102,15 +103,9 @@ class Angle_distribution(AnalysisBase):
             np.savetxt("angle_distribution.dat", conbined_data, header="angle\tw_suf_dist\toh_suf_dist", fmt='%.5f', delimiter='\t')
 
 
-@click.command(name="angle")
-@click.argument("filename", type=click.Path(exists=True))
-@click.option('--cell', type=arg_type.Cell, help="set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c")
+@click.command(name="angle", help="analysis angle between normal vectors and OH vector or bisector")
+@common_setting
 @click.option("--water_height", type=float, help="water height from surface")
-@click.option("--surface", type=str, help="surface group")
-@click.option('--update_water', is_flag=True, help='update water with distance or angle judgment')
-@click.option('--distance', type=float, help='update water distance judgment', default=1.2, show_default=True)
-@click.option('--angle', type=(float, float), help='update water angle judgment')
-@click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')
 def main(filename, cell, water_height, update_water, distance, angle, surface, r):
     """analysis angle between normal vectors and OH vector or bisector"""
     a = Angle_distribution(filename, cell, water_height, update_water, distance_judg=distance, angle_judg=angle, surface=surface)

mdkits/md_cli/density.py

@@ -10,6 +10,7 @@ from mdkits.util import (
     encapsulated_mda,
     os_operation,
 )
+from .setting import common_setting
 import warnings, sys
 warnings.filterwarnings("ignore")
 
@@ -79,9 +80,10 @@ class Density_distribution(AnalysisBase):
             self._append(group.positions[:, 2])
 
         if self.surface_group:
-            lower_z, upper_z = numpy_geo.find_surface(self.surface_group.positions[:, 2], layer_tolerance=1, surface_tolerance=5)
-            self.surface_pos[0] += lower_z
-            self.surface_pos[1] += upper_z
+            surface = numpy_geo.find_surface(self.surface_group.positions[:, 2])
+            self.surface_pos[0] += surface[0]
+            if len(surface) > 1:
+                self.surface_pos[1] += surface[1]
 
         self.frame_count += 1
 
@@ -98,7 +100,8 @@ class Density_distribution(AnalysisBase):
 
             if self.surface:
                 lower_z = self.surface_pos[0] / self.frame_count
-                upper_z = self.surface_pos[1] / self.frame_count
+                if self.surface_pos[1] == 0:
+                    upper_z = np.inf
 
                 mask = (bins_z >= lower_z) & (bins_z <= upper_z)
                 filtered_bins_z = bins_z[mask] - lower_z
@@ -110,16 +113,11 @@ class Density_distribution(AnalysisBase):
 
             np.savetxt(self.o, conbined_data, header="Z\tdensity", fmt='%.5f', delimiter='\t')
 
-@click.command(name='density')
-@click.argument('filename', type=click.Path(exists=True), default=os_operation.default_file_name('*-pos-1.xyz', last=True))
-@click.option('--cell', type=arg_type.Cell, help='set cell from cp2k input file or a list of lattice: --cell x,y,z or x,y,z,a,b,c', default='input.inp', show_default=True)
-@click.option('--element', type=str, help='element to analysis')
+@click.command(name='density', help="analysis density or concentration of element in a trajectory file")
+@common_setting
+@click.option('--group', type=str, help='group to analysis')
 @click.option('--atomic_mass', type=float, help='output density unit (g/cm3), should give atomic mass of element, else is concentration unit (mol/L)')
 @click.option('-o', type=str, help='output file name', default='density_{element}.dat', show_default=True)
-@click.option('--update_water', is_flag=True, help='update water with distance or angle judgment')
-@click.option('--distance', type=float, help='update water distance judgment', default=1.2, show_default=True)
-@click.option('--angle', type=(float, float), help='update water angle judgment')
-@click.option('--surface', type=str, help='surface element')
 def main(filename, cell, o, element, atomic_mass, update_water, distance, angle, surface):
     """
     analysis density or concentration of element in a trajectory file

mdkits/md_cli/dipole.py

@@ -0,0 +1,120 @@
+import numpy as np
+import click
+import MDAnalysis
+from MDAnalysis import Universe
+from MDAnalysis.analysis.base import AnalysisBase
+from mdkits.util import (
+    arg_type,
+    numpy_geo,
+    encapsulated_mda,
+    os_operation
+)
+from .setting import common_setting
+import sys
+
+
+class Dipole_distribution(AnalysisBase):
+    def __init__(self, filename, cell, update_water, distance_judg, angle_judg, surface, dt=0.001, bin_size=0.2):
+        u = Universe(filename)
+        u.trajectory.ts.dt = dt
+        u.dimensions = cell
+
+        self.u = u
+        self.atomgroup = u.select_atoms("all")
+        self.bin_size = bin_size
+        self.frame_count = 0
+        self.surface = surface
+        self.update_water = update_water
+        self.mid_z = u.dimensions[2] / 2
+
+        if self.update_water:
+            self.distance_judg = distance_judg
+            self.angle_judg = angle_judg
+
+        if surface is not None:
+            self.surface_group = self.atomgroup.select_atoms(f"{surface}")
+            if self.surface_group.n_atoms == 0:
+                sys.exit("Please specify the correct surface group")
+        else:
+            self.surface_group = False
+
+        super(Dipole_distribution, self).__init__(self.atomgroup.universe.trajectory, verbose=True)
+
+    def _prepare(self):
+        self.bin_num = int(self.u.dimensions[2] / self.bin_size) + 2
+        self.dipole_distribution = np.zeros(self.bin_num, dtype=np.float64)
+        self.o_count = np.zeros(self.bin_num, dtype=np.float64)
+
+        if self.surface_group:
+            self.surface_pos = np.zeros(2)
+
+    def _append(self, angle, z):
+        bins = np.floor(z / self.bin_size).astype(int) + 1
+        np.add.at(self.dipole_distribution, bins, angle)
+        np.add.at(self.o_count, bins , 1)
+
+    def _single_frame(self):
+        o_group = self.atomgroup.select_atoms("name O")
+
+        if self.update_water:
+            h_group = self.atomgroup.select_atoms("name H")
+            o, oh1, oh2 = encapsulated_mda.update_water(self, o_group, h_group, distance_judg=self.distance_judg, angle_judg=self.angle_judg, return_index=False)
+        else:
+            o = o_group
+            oh1 = self.atomgroup[o.indices + 1]
+            oh2 = self.atomgroup[o.indices + 2]
+
+        if self.surface_group:
+            lower_z, upper_z = numpy_geo.find_surface(self.surface_group.positions[:, 2])
+            self.surface_pos[0] += lower_z
+            self.surface_pos[1] += upper_z
+
+        vec1 = MDAnalysis.lib.distances.minimize_vectors(oh1.positions - o.positions, self.u.dimensions)
+        vec2 = MDAnalysis.lib.distances.minimize_vectors(oh2.positions - o.positions, self.u.dimensions)
+
+        bisector = numpy_geo.vector_between_two_vector(vec1, vec2)
+
+
+        angle_bisector = np.hstack((bisector[o.positions[:, 2] < self.mid_z][:, 2] / np.linalg.norm(bisector[o.positions[:, 2] < self.mid_z], axis=1), -bisector[o.positions[:, 2] > self.mid_z][:, 2] / np.linalg.norm(bisector[o.positions[:, 2] > self.mid_z], axis=1)))
+
+        self._append(angle_bisector, np.hstack((o.positions[:, 2][o.positions[:, 2] < self.mid_z], o.positions[:, 2][o.positions[:, 2] > self.mid_z])))
+
+        self.frame_count += 1
+
+    def _conclude(self):
+        if self.frame_count > 0:
+            average_dipole = self.dipole_distribution / self.o_count
+            water_density = (self.o_count * (15.999+1.0008*2) * 1.660539 / (self.u.dimensions[0] * self.u.dimensions[1] * self.bin_size)) / self.frame_count
+            average_dipole = average_dipole * water_density
+            bins_z = np.arange(len(average_dipole)) * self.bin_size
+
+            if self.surface:
+                lower_z, upper_z = self.surface_pos / self.frame_count
+
+                mask = (bins_z >= lower_z) & (bins_z <= upper_z)
+                filtered_bins_z = bins_z[mask] - lower_z
+                filtered_dipole_distribution = average_dipole[mask]
+
+                conbined_data = np.column_stack((filtered_bins_z, filtered_dipole_distribution))
+            else:
+                conbined_data = np.column_stack((bins_z, average_dipole))
+
+            np.savetxt("dipole_distribution.dat", conbined_data, header="z\tDipole Z Positions\tWater Density", fmt='%.5f', delimiter='\t')
+
+
+@click.command(name="dipole")
+@common_setting
+def main(filename, cell, update_water, distance, angle, surface, r):
+    """analysis dipole along z-axis"""
+    a = Dipole_distribution(filename, cell, update_water, distance_judg=distance, angle_judg=angle, surface=surface)
+    if r is not None:
+        if len(r) == 2:
+            a.run(start=r[0], stop=r[1])
+        elif len(r) == 3:
+            a.run(start=r[0], stop=r[1], step=r[2])
+    else:
+        a.run()
+
+
+if __name__ == "__main__":
+    main()

mdkits/md_cli/hb_distribution.py

@@ -7,6 +7,7 @@ from MDAnalysis import Universe
 from MDAnalysis.analysis.base import AnalysisBase
 from mdkits.util import arg_type, os_operation, numpy_geo, encapsulated_mda
 import warnings, sys
+from .setting import common_setting
 warnings.filterwarnings("ignore")
 
 
@@ -120,23 +121,27 @@ class Hb_distribution(AnalysisBase):
             self._append(hb_d, hb_a, o_group.positions[:, 2])
 
         if self.surface_group:
-            lower_z, upper_z = numpy_geo.find_surface(self.surface_group.positions[:, 2])
-            self.surface_pos[0] += lower_z
-            self.surface_pos[1] += upper_z
+            surface = numpy_geo.find_surface(self.surface_group.positions[:, 2])
+            self.surface_pos[0] += surface[0]
+            if len(surface) > 1:
+                self.surface_pos[1] += surface[1]
 
         self.frame_count += 1
 
     def _conclude(self):
         if self.frame_count > 0 and self.index is None:
             average_od = self.od / self.frame_count
-            average_donor = (self.donor / self.frame_count) / average_od
-            average_accepter = (self.accepter / self.frame_count) / average_od
+            average_donor = np.nan_to_num((self.donor / self.frame_count) / average_od, nan=0)
+            average_accepter = np.nan_to_num((self.accepter / self.frame_count) / average_od, nan=0)
             average_sum = average_donor + average_accepter
 
             bins_z = np.arange(len(self.donor)) * self.bin_size
 
             if self.surface:
-                lower_z, upper_z = self.surface_pos/self.frame_count
+                surface = self.surface_pos/self.frame_count
+                lower_z = surface[0]
+                if surface[1] ==0:
+                    upper_z = np.inf
                 mask = (bins_z >= lower_z) & (bins_z <= upper_z)
                 filtered_bins_z = bins_z[mask] - lower_z
                 filtered_average_accepter = average_accepter[mask]
@@ -158,15 +163,9 @@ class Hb_distribution(AnalysisBase):
             print(output)
 
 
-@click.command(name="hb")
-@click.argument('filename', type=click.Path(exists=True), default=os_operation.default_file_name('*-pos-1.xyz', last=True))
+@click.command(name="hb", help="analysis hydrogen bond distribution along z-axis")
+@common_setting
 @click.option('--hb_param', type=click.Tuple([float, float]), help='parameter for hydrogen bond', default=(3.5, 35), show_default=True)
-@click.option('--cell', type=arg_type.Cell, help='set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c')
-@click.option('--surface', type=str, help='surface element')
-@click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')
-@click.option('--update_water', is_flag=True, help='update water with distance or angle judgment')
-@click.option('--distance', type=float, help='update water distance judgment', default=1.2, show_default=True)
-@click.option('--angle', type=(float, float), help='update water angle judgment')
 @click.option('--index', type=int, help='index of an atom')
 def main(filename, hb_param, cell, surface, r, update_water, distance, angle, index):
     """analysis hydrogen bond distribution along z-axis"""

mdkits/md_cli/md_cli.py

@@ -1,21 +1,30 @@
 import click
 from mdkits.md_cli import (
+    wrap,
+    dipole,
+    angle,
     density,
     hb_distribution,
-    angle,
+    rdf,
+    msd,
+    monitor,
 )
 
 
 @click.group(name='md')
 @click.pass_context
-def main(ctx):
+def cli(ctx):
     """kits for MD analysis"""
-    pass
 
-main.add_command(density.main)
-main.add_command(hb_distribution.main)
-main.add_command(angle.main)
+cli.add_command(wrap.main)
+cli.add_command(density.main)
+cli.add_command(dipole.main)
+cli.add_command(angle.main)
+cli.add_command(hb_distribution.main)
+cli.add_command(rdf.main)
+cli.add_command(msd.main)
+cli.add_command(monitor.main)
 
 
 if __name__ == '__main__':
-    main()
+    cli()

mdkits/md_cli/monitor.py

@@ -0,0 +1,104 @@
+import click
+from .setting import common_setting
+import MDAnalysis
+from MDAnalysis import Universe
+from MDAnalysis.analysis.base import AnalysisBase
+from mdkits.util import arg_type, numpy_geo
+import numpy as np
+import sys
+
+
+class Monitor(AnalysisBase):
+    def __init__(self, filename, cell, index, surface, dt=0.001):
+        u = Universe(filename)
+        u.trajectory.ts.dt = dt
+        u.dimensions = cell
+
+        self.u = u
+        self.atomgroup = self.u.select_atoms("all")
+        self.surface = surface
+
+        if index is None:
+            sys.exit("Please specify at least one atom to monitor")
+        else:
+            self.index = index
+            self.group = " or ".join([ f"index {i}" for i in self.index ])
+
+        if surface is not None:
+            self.surface_group = self.atomgroup.select_atoms(f"{surface}")
+            if self.surface_group.n_atoms == 0:
+                sys.exit("Please specify the correct surface group")
+        else:
+            self.surface_group = False
+
+        super(Monitor, self).__init__(self.atomgroup.universe.trajectory, verbose=True)
+
+    def _prepare(self):
+        self.height = []
+        if len(self.index) == 2:
+            self.distance = []
+        elif len(self.index) == 3:
+            self.distance = []
+            self.angle = []
+    
+    def _single_frame(self):
+        if self.surface_group:
+            surface = numpy_geo.find_surface(self.surface_group.positions[:, 2])
+        else:
+            surface = [0]
+
+        self.height.append(self.atomgroup.select_atoms(self.group).positions[:, 2] - surface[0])
+
+        if len(self.index) == 2:
+            vec = MDAnalysis.lib.distances.minimize_vectors(self.atomgroup[self.index[0]].position - self.atomgroup[self.index[1]].position, self.u.dimensions)
+
+            self.distance.append(np.linalg.norm(vec))
+
+        if len(self.index) == 3:
+            vec1 = MDAnalysis.lib.distances.minimize_vectors(self.atomgroup[self.index[0]].position - self.atomgroup[self.index[1]].position, self.u.dimensions)
+            vec2 = MDAnalysis.lib.distances.minimize_vectors(self.atomgroup[self.index[2]].position - self.atomgroup[self.index[1]].position, self.u.dimensions)
+
+            self.distance.append(np.array([np.linalg.norm(vec1), np.linalg.norm(vec2)]))
+            self.angle.append(numpy_geo.vector_vector_angle(vec1, vec2))
+
+    def _conclude(self):
+        frame_count = np.arange(self.u.trajectory.n_frames).reshape(-1, 1)
+
+        self.height = np.vstack(self.height)
+
+        np.savetxt("monitor.dat", np.hstack((frame_count, self.height)), fmt="%.5f", header=f"frame\t{'  '.join(self.atomgroup.select_atoms(self.group).names)}")
+
+        if len(self.index) == 2:
+            self.distance = np.vstack(self.distance)
+
+            np.savetxt("monitor.dat", np.hstack((frame_count, self.height, self.distance)), fmt="%.5f", header=f"frame\t\t{'  '.join(self.atomgroup.select_atoms(self.group).names)}\t{self.atomgroup.names[self.index[0]]}-{self.atomgroup.names[self.index[1]]}")
+        elif len(self.index) == 3:
+            self.distance = np.vstack(self.distance)
+            self.angle = np.vstack(self.angle)
+
+            np.savetxt("monitor.dat", np.hstack((frame_count, self.height, self.distance, self.angle)), fmt="%.5f", header=f"frame\t\t{'  '.join(self.atomgroup.select_atoms(self.group).names)}\t{self.atomgroup.names[self.index[0]]}-{self.atomgroup.names[self.index[1]]}\t{self.atomgroup.names[self.index[2]]}-{self.atomgroup.names[self.index[1]]}\t{self.atomgroup.names[self.index[0]]}-{self.atomgroup.names[self.index[1]]}-{self.atomgroup.names[self.index[2]]}")
+
+
+@click.command(name="monitor")
+@click.argument("filename", type=click.Path(exists=True))
+@click.option("--index", "-i", type=int, help="index of atom to monitor", multiple=True)
+@click.option('--cell', type=arg_type.Cell, help="set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c")
+@click.option("--surface", type=str, help="surface group")
+@click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')
+def main(filename, cell, index, surface, r):
+    """
+    monitor the property of between atoms
+    """
+    a = Monitor(filename, cell, index, surface)
+    if r is not None:
+        if len(r) == 2:
+            a.run(start=r[0], stop=r[1])
+        elif len(r) == 3:
+            a.run(start=r[0], stop=r[1], step=r[2])
+    else:
+        a.run()
+    
+    
+
+if __name__ == "__main__":
+    main()

mdkits/md_cli/msd.py

@@ -0,0 +1,30 @@
+import click
+import MDAnalysis as mda
+import MDAnalysis.analysis.msd as msd
+import numpy as np
+
+
+@click.command(name="msd")
+@click.argument("filename", type=click.Path(exists=True))
+@click.argument('type', type=click.Choice(['xyz', 'xy', 'yz', 'xz', 'x', 'y', 'z']))
+@click.argument("group", type=str)
+def main(filename, type, group):
+    """analysis msd along the given axis"""
+    u = mda.Universe(filename)
+    MSD = msd.EinsteinMSD(u, select=group, msd_type=type, fft=True)
+    MSD.run(verbose=True)
+
+    data = np.arange(1, MSD.n_frames + 1).reshape(-1, 1)
+    s = "_"
+    name = f"{s.join(group.split(' '))}"
+    header = ''
+    for i in range(MSD.n_particles):
+        data = np.concatenate((data, MSD.results.msds_by_particle[:, i].reshape(-1, 1)), axis=1)
+        header += name + f"_{i}\t"
+
+    np.savetxt(f"msd_{type}.dat", data, fmt="%.5f", delimiter="\t", header=f"frame\t{header}")
+
+
+
+if __name__ == '__main__':
+    main()

mdkits/md_cli/rdf.py

@@ -0,0 +1,39 @@
+import MDAnalysis as mda
+from MDAnalysis.analysis import rdf
+import numpy as np
+import click
+from mdkits.util import arg_type
+
+
+@click.command(name="rdf")
+@click.argument("filename", type=click.Path(exists=True))
+@click.option('--cell', type=arg_type.Cell, help='set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c')
+@click.option("--group", type=click.Tuple([str, str]), help="two group to analysis")
+@click.option('--range', type=click.Tuple([float, float]), help="the range of rdf")
+@click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')
+def main(filename, cell, group, range, r):
+    """analysis the radial distribution function"""
+    u = mda.Universe(filename)
+    u.trajectory.ts.dt = 0.0001
+    u.dimensions = cell
+    o = f"rdf_{'_'.join(group).replace(' ', '_')}.dat"
+
+    group1 = u.select_atoms(group[0])
+    group2 = u.select_atoms(group[1])
+
+    crdf = rdf.InterRDF(group1, group2, verbose=True, range=(range[0], range[1]), norm='density')
+
+    if r is not None:
+        if len(r) == 2:
+            crdf.run(start=r[0], stop=r[1])
+        elif len(r) == 3:
+            crdf.run(start=r[0], stop=r[1], step=r[2])
+    else:
+        crdf.run()
+
+    combin = np.column_stack((crdf.results.bins, crdf.results.rdf))
+    np.savetxt(o, combin, header="A\tgr", fmt="%.5f", delimiter='\t')
+
+
+if __name__ == "__main__":
+    main()

mdkits/md_cli/setting.py

@@ -0,0 +1,14 @@
+import click
+from mdkits.util import arg_type, os_operation
+
+
+def common_setting(f):
+    f = click.argument('filename', type=click.Path(exists=True), default=os_operation.default_file_name('*-pos-1.xyz', last=True))(f)
+    f = click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')(f)
+    f = click.option('--angle', type=(float, float), help='update water angle judgment')(f)
+    f = click.option('--distance', type=float, help='update water distance judgment', default=1.2, show_default=True)(f)
+    f = click.option('--update_water', is_flag=True, help='update water with distance or angle judgment')(f)
+    f = click.option("--surface", type=str, help="surface group")(f)
+    f = click.option('--cell', type=arg_type.Cell, help="set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c")(f)
+
+    return f

mdkits/{cli → md_cli}/wrap.py

@@ -28,7 +28,7 @@ def main(filename, o, cell):
             ag.wrap()
             W.write(ag)
 
-    click.echo("\nwrap is done, output file {o} is:")
+    click.echo(f"\nwrap is done, output file {o} is:")
     click.echo(os.path.abspath(o))
 
 

mdkits/mdkits.py

@@ -4,7 +4,6 @@ from mdkits.dft_cli import dft_cli
 from mdkits.md_cli import md_cli
 from mdkits.cli import (
     convert,
-    wrap,
     extract,
     data,
     plot,
@@ -19,11 +18,10 @@ def cli(ctx):
     pass
 
 
-cli.add_command(md_cli.main)
-cli.add_command(dft_cli.main)
+cli.add_command(md_cli.cli)
 cli.add_command(build_cli.cli_build)
+cli.add_command(dft_cli.main)
 cli.add_command(convert.main)
-cli.add_command(wrap.main)
 cli.add_command(extract.main)
 cli.add_command(data.main)
 cli.add_command(plot.main)

mdkits/util/arg_type.py

@@ -6,7 +6,7 @@ from mdkits.util import os_operation, cp2k_input_parsing, out_err
 
 
 class CellType(click.ParamType):
-    name = "pbc cell type"
+    name = "cell type"
 
     def convert(self, value, param, ctx):
         if isinstance(value, str):
@@ -36,7 +36,7 @@ class FrameRangeType(click.ParamType):
 
 
 class StructureType(click.ParamType):
-    name = "structure file type"
+    name = "structure type"
     def convert(self, value, param, ctx):
         no_cell=np.array([0., 0., 0., 90., 90., 90.])
         if isinstance(value, str):

mdkits/util/numpy_geo.py

@@ -45,7 +45,10 @@ def vector_between_two_vector(vector1, vector2):
 
 
 def vector_vector_angle(vector, surface_vector):
-    cos = np.dot(vector, surface_vector) / (np.linalg.norm(vector, axis=1) * np.linalg.norm(surface_vector))
+    if len(vector.shape) == 1:
+        cos = np.dot(vector, surface_vector) / (np.linalg.norm(vector) * np.linalg.norm(surface_vector))
+    else:
+        cos = np.dot(vector, surface_vector) / (np.linalg.norm(vector, axis=1) * np.linalg.norm(surface_vector))
     vector_vector_angle = np.arccos(np.clip(cos, -1.0, 1.0))
     vector_vector_angle = np.degrees(vector_vector_angle)
     return vector_vector_angle

{mdkits-0.1.29.dist-info → mdkits-0.1.30.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.29
+Version: 0.1.30
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -21,102 +21,144 @@ Requires-Dist: julia (>=0.6.2,<0.7.0)
 Requires-Dist: matplotlib (>=3.9.0,<4.0.0)
 Requires-Dist: numpy (>=1.26.4,<2.0.0)
 Requires-Dist: pyyaml (>=6.0.1,<7.0.0)
+Requires-Dist: tidynamics (>=1.1.2,<2.0.0)
 Project-URL: Repository, https://github.com/jxxcr/mdkits
 Description-Content-Type: text/markdown
 
-# MD 轨迹分析脚本
+# mdkits
 `mdkits` 提供了多种工具, 安装脚本:
 ```bash
 pip install mdkits --upgrade
 ```
+## 通用的选项参数类型
+1. `CELL TYPE`: 指定晶胞参数, 如`10,10,10`, `10,10,10,90,90,90`等
+2. `FRAME RANGE`: 指定帧范围, 如`1`, `1:10:2`等
+3. `--group`和`--surface`: 按[选择语言](https://userguide.mdanalysis.org/stable/selections.html)选取分析对象
+4. `--update_water`, `--distance` 和 `--angle`: 在分析轨迹的过程中开启动态更新水分子的功能
 
+## 轨迹文件处理脚本
+`md`为轨迹文件处理工具, 其中包含多个处理工具
 ### 密度分布
-`density`用于分析体系中的某种元素沿z轴的密度分布, 如分析体系中的`O`元素沿z轴的密度分布, `--element`选项指定元素使用`MDAnalysis`的[选择语言](https://userguide.mdanalysis.org/stable/selections.html):
+`density`用于分析体系中的某种元素沿z轴的密度分布, 如分析体系中的`O`元素沿z轴的密度分布:
 ```bash
-mdkits density [FILENAME] --element="name H" --cell [FILENAME]
+mdkits md density [FILENAME] --group="name H" --cell [FILENAME]
 ```
 这样会输出一个文件名为`density_name_H.dat`的文件, 第一列为z轴坐标, 第二列为浓度分布, 单位为 mol/L. 如果想输出为单位为 $g/cm^3$ 的密度分布, 可以指定`--atomic_mass` 选项, 如:
 ```bash
-mdkits density [FILENAME] --element="name H" --cell [FILENAME] --atomic_mass=1.00784
+mdkits md density [FILENAME] --group="name H" --cell [FILENAME] --atomic_mass=1.00784
 ```
 则输出单位为 $g/cm^3$ 的密度分布. 可以指定表面原子来将密度分布归一化到表面, 如:
 ```bash
-mdkits density [FILENAME] --element="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+mdkits md density [FILENAME] --group="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
 ```
 这样会将密度分布归一化到表面, 同时以O原子的位置作为水分子的位置分析处理水分子的密度分布. 对于体系中存在 $OH^-$ 离子的体系可以使用`--update_water`的选项在每一帧更新水分子的位置, 不需要额外指定元素, 如:
 ```bash
-mdkits density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+mdkits md density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
 ```
 输出的文件名为`density_water.dat`.
 
 ### 氢键
-
-#### 单个水分子
-
-#### 氢键分布
+`hb`用于分析体系中的氢键, 如分析体系中的氢键在z轴上的分布:
+```bash
+mdkits md hb [FILENAME] --cell 10,10,40 --surface "prop z < 10" --update_water
+```
+或分析单个水分子的氢键:
+```bash
+mdkits md hb [FILENAME] --cell 10,10,40 --index 15
+```
 
 ### 角度
+`angel`用于分析水分子中的二分向量和OH向量与表面法向量的夹角的丰度分布, 如分析距离表面 5 Å 的水分子的角度丰度分布:
+```bash
+mdkits md angle [FILENAME] --cell 10,10,40 --surface "name Pt" --water_height 5
+```
 
-#### 与表面法向量夹角分布
+### 偶极分布
+`diople`用于分析体系中的偶极($\cos \phi \rho_{H_2 O}$)分布, 如分析体系中的 $\cos \phi \rho_{H_2 O}$ 分布:
+```bash
+mdkits md diople [FILENAME] --cell 10,10,40 --surface "name Pt"
+```
 
-#### ion - O - ion 夹角分布
+### 径向分布函数(RDF)
+`rdf`用于分析两个`group`之间的径向分布函数, 如分析体系中的`O`元素与`H`元素之间的径向分布函数:
+```bash
+mdkits md rdf [FILENAME] --group "name O" "name H" --cell 10,10,40 --range 0.1 5
+```
 
-#### $\cos \phi \rho_{H_2 O}$ 分布
+### 均方位移(MSD)
+`msd`用于分析体系中某些原子的均方位移, 如分析体系中`Li`原子在z轴上的均方位移:
+```bash
+mdkits md msd [FILENAME] z "name Li"
+```
 
-### RDF
+### 监控
+`monitor`用于监控体系中原子高度, 键长和键角的变化, 如监控`index`为0的原子的高度:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0
+```
+会输出0距离表面的高度随每一帧的变化, 如监控0-1的键长:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0 -i 1
+```
+会输出0和1距离表面的高度和0-1之间的键长随每一帧的变化, 如监控1-0-2的键角:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 1 -i 0 -i 2
+```
+会输出1, 0, 2距离表面的高度, 1-0和0-2的键长和1-0-2的键角随每一帧的变化, 注意位于角上的原子应该放在中间
 
 ### 位置归一化
 `wrap`用于将轨迹文件中的原子位置进行归一化处理, 如将`[FILENAME]`中的原子位置归一化到晶胞中, 并输出为`wrapped.xyz`, 默认从`cp2k`的输出文件`input_inp`中读取`ABC`和`ALPHA_BETA_GAMMA`信息作为晶胞参数:
 ```bash
-mdkits wrap [FILENAME] 
+mdkits md wrap [FILENAME] 
 ```
 或指定`cp2k`的输入文件:
 ```bash
-mdkits wrap [FILENAME] --cp2k_input_file setting.inp
+mdkits md wrap [FILENAME] --cp2k_input_file setting.inp
 ```
 或指定晶胞参数:
 ```bash
-mdkits wrap [FILENAME] --cell 10,10,10
+mdkits md wrap [FILENAME] --cell 10,10,10
 ```
 默认的`[FILENAME]`为`*-pos-1.xyz`
 
 ## DFT 性质分析脚本
+`dft`为DFT性质分析工具, 其中包含多个分析工具
 ### PDOS
 `pdos`用于分析体系中的pdos, 分析[FILENAME]的d轨道的dos:
 ```bash
-mdkits pdos [FILENAME] -t d
+mdkits dft pdos [FILENAME] -t d
 ```
 
 ### CUBE 文件
 `cube`用于处理[`cube`格式](https://paulbourke.net/dataformats/cube/)的文件, 将其在z轴上进行平均:
 ```bash
-mdkits cube [FILENAME]
+mdkits dft cube [FILENAME]
 ```
 分析好的数据会输出为`cube.out`, 可以同时计算一个区域内的平均值:
 ```bash
-mdkits cube [FILENAME] -b 1 2
+mdkits dft cube [FILENAME] -b 1 2
 ```
 会将平均值打印在屏幕上, 同时记录在`cube.out`中的注释行.
 
 ## 建模
-`build`为界面的工具, 其中包含多个建模工具
+`build`为建模的工具, 其中包含多个建模工具
 
 ### 构建体相模型
 `bulk`用于构建体相模型, 如构建`Pt`的`fcc`体相模型:
 ```bash
-mdkits build_bulk Pt fcc
+mdkits build bulk Pt fcc
 ```
 构建为常胞模型:
 ```bash
-mdkits build_bulk Pt fcc --cubic
+mdkits build bulk Pt fcc --cubic
 ```
 构建一个`Caesium chloride`结构的模型:
 ```bash
-mdkits build_bulk CsCl cesiumchloride -a 4.123
+mdkits build bulk CsCl cesiumchloride -a 4.123
 ```
 构建一个`fluorite `结构的模型:
 ```bash
-mdkits build_bulk BaF2 fluorite -a 6.196
+mdkits build bulk BaF2 fluorite -a 6.196
 ```
 
 ### 构建表面模型
@@ -133,6 +175,60 @@ mdkits build surface Pt fcc111 2 2 3 --vacuum 15
 mdkits build surface C2 graphene 3 3 1 --vacuum 15
 ```
 
+### 从现有结构中构建表面模型
+`cut`用于从现有的结构中构建表面模型(模型必须为常胞模型), 如从`Pt_fcc.cif`中构建`fcc331`表面模型:
+```bash
+mdkits build cut Pt_fcc.cif --face 3 3 1 --size 3 3 5 --vacuum 15
+```
+
+### 在表面结构上添加吸附物
+`adsorbate`用于在表面结构上添加吸附物, 如在`surface.cif`上添加`H`原子:
+```bash
+mdkits build adsorbate surface.cif H --select "index 0" --height 1    
+```
+或在`Pt_fcc111_335.cif`上添加覆盖度为5的`H`原子:
+```bash
+mdkits build adsorbate Pt_fcc111_335.cif H --select "prop z > 16" --height 2 --cover 5
+```
+
+### 构建溶液相模型
+`solution`用于构建溶液相模型, 初次使用时应先安装`juliaup`:
+```bash
+mdkits build solution --install_julia
+```
+然后安装`Packmol`:
+```bash
+mdkits build solution --install_packmol
+```
+成功安装后就可以使用`solution`功能了, 如构建一个32个水分子的水盒子:
+```bash
+mdkits build solution --water_number 32 --cell 9.86,9.86,9.86
+```
+或构建一个含有离子的溶液:
+```bash
+mdkits build solution li.xyz k.xyz --water_number 64 --tolerance 2.5 -n 25 -n 45 --cell 15,15,15
+```
+其中`-n`的个数必须与指定的溶剂分子种类数量一致, 用于分别指定添加的溶剂的数量. 或者从`packmol`的输入文件中构建溶液相模型:
+```bash
+mdkits build solution input.pm input2.pm  --infile
+```
+
+### 构建界面模型
+`interface`用于构建界面模型, 如构建一个没有真空的界面模型:
+```bash
+mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif
+```
+或构建一个带有气相模型的界面:
+```bash
+mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif --cap ne --vacuum 20
+```
+
+### 构建超胞模型
+`supercell`用于构建超胞模型:
+```bash
+mdkits build supercell Li3PO4.cif 2 2 2
+```
+
 ## 其他
 ### 轨迹提取
 `extract`用于提取轨迹文件中的特定的帧, 如从`frames.xyz`中提取第 1000 帧到第 2000 帧的轨迹文件, 并输出为`1000-2000.xyz`, `-r`选项的参数与`Python`的切片语法一致:

{mdkits-0.1.29.dist-info → mdkits-0.1.30.dist-info}/RECORD

@@ -1,11 +1,11 @@
 mdkits/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mdkits/build_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mdkits/build_cli/adsorbate.py,sha256=Zp21i-miFv5zQlYjZnZuVpMxvNVT-6RtdlaoWDMwaOg,1900
+mdkits/build_cli/adsorbate.py,sha256=9D_IYpnXd30pALC6JIvVPPxuxDfpsoArgMhE2hSeOSw,1947
 mdkits/build_cli/build_bulk.py,sha256=o3SFov5Ggk-qKcy6-NBoIYKvZV24OhcH3-du1d0U6H4,1593
 mdkits/build_cli/build_cli.py,sha256=sqjnq5aHWLYLbNzN5SORkEYeYaewLagFuSvspJxyh7E,725
 mdkits/build_cli/build_interface.py,sha256=3EDxUb-vGHFuat1Ex_wojVsN8PtzHiGrnDQIEa9WZ60,2448
 mdkits/build_cli/build_solution.py,sha256=7bwaDH-vLBNRzGoYXT72bzLVXdQAZ4HXNuUDuR7AI78,5377
-mdkits/build_cli/build_surface.py,sha256=cBEQ-KR_6j-Mcsxrwvzyl6p1SiY_chIytrCu7MS3q08,2794
+mdkits/build_cli/build_surface.py,sha256=9GGpmQlCG6vxNevMyWcfI2EL_JiAAKIhxNokZyEzVLU,2739
 mdkits/build_cli/cut_surface.py,sha256=_f0t2OyBKb8ZV04b3GezfSDUN4XFd5kQM-yWbSmOofs,2742
 mdkits/build_cli/supercell.py,sha256=3iTTt3DHaERWDFonhBRS0oqWhjFh6pbS5SpIR-O1gYg,1034
 mdkits/build_cli/water.xyz,sha256=ByLDz-rYhw_wLPBU78lIQHe4s4Xf5Ckjft-Dus3czIc,171
@@ -18,30 +18,35 @@ mdkits/cli/hartree_potential_ave.py,sha256=25oy3QsgIdxrTFpTqpnGvLAheb-d6poeLMN7i
 mdkits/cli/hb.py,sha256=lADr4tlctbtQ3_f_UpznkLnSI0MJlAT-pknEf_dwrnU,5330
 mdkits/cli/packmol_input.py,sha256=76MjjMMRDaW2q459B5mEpXDYSSn14W-JXudOOsx-8E4,2849
 mdkits/cli/plot.py,sha256=1yh5dq5jnQDuyWlxV_9g5ztsnuFHVu4ouYQ9VJYSrUU,8938
-mdkits/cli/wrap.py,sha256=AUxGISuiCfEjdMYl-TKc2VMCPHSybWKrMIOTn_6kSp0,1043
 mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
 mdkits/dft_cli/cube.py,sha256=G-QNup8W6J1-LCcEl1EHsV3nstd23byePDOcE_95t18,1176
 mdkits/dft_cli/dft_cli.py,sha256=Ou9-e4uGhDJJk2Gdg7tcj6iKApkAJZFSbN1hr7SlCMc,281
 mdkits/dft_cli/pdos.py,sha256=ALAZ5uOaoT0UpCyKYleWxwmk569HMzKTTK-lMJeicM8,1411
-mdkits/md_cli/angle.py,sha256=PaqFnlVnWHy6t6eDOQdq7J0jhMpCnekIzNCjhTMpdqw,5930
-mdkits/md_cli/density.py,sha256=-o1argCiwWr9mjggeetuX0sDMxjhRSPMG25sOS3KZYU,5574
-mdkits/md_cli/hb_distribution.py,sha256=MPrYfVW0MC01G1GZTxTca58jSlD0rVRnR1g1DmvdE00,8301
-mdkits/md_cli/md_cli.py,sha256=7hefzX0NIydlL2AjqTkTwLUg6yIOMSCn3zQ1zU9pP3s,348
-mdkits/mdkits.py,sha256=UGCAbVml8MdXXG--LGo8BUm9BXofg9P3HKIEDTUbd48,635
+mdkits/md_cli/angle.py,sha256=cfhI6dsn_hIy-YXSTXemu1m1O_l2HuL_x6zx_3uL-Uw,5450
+mdkits/md_cli/density.py,sha256=_w6UunY6alTp0jLa8cyqR8sSYubN0XbM-PDF4SkzsJU,5058
+mdkits/md_cli/dipole.py,sha256=tXTO8CZAQTVY55GwuXWJNGo7EQ4Tb2611g5IHucdlec,4836
+mdkits/md_cli/hb_distribution.py,sha256=x5QC6X0TBkN_9jRazDuxjzOzLDiZKIyBxTroueYbG5g,7921
+mdkits/md_cli/md_cli.py,sha256=YOz4qJuYIfJAv-vt0xkw2gopkxGGN7JPp86_dXgPVz8,534
+mdkits/md_cli/monitor.py,sha256=JNEgz5RGbFn4x_E85pAiPUY1NVIyZ3b2vjpBk_d1dR8,4536
+mdkits/md_cli/msd.py,sha256=v-9TPKBGHz6ce2PUwexrekVq_9eiutIOQYaw582yN30,965
+mdkits/md_cli/rdf.py,sha256=u-euWDKpWC4VkZJFBFPqBFJLkLC3nzpfcf1dmf_aBiw,1402
+mdkits/md_cli/setting.py,sha256=mxMTYpm6DUjMt9hOKsJbBSKwCqzMilOR0bo1azSdJP0,846
+mdkits/md_cli/wrap.py,sha256=YdUpvhRyKn7bYnIAVgP39qItPdrEoTeJl55TmbS7Qqk,1044
+mdkits/mdkits.py,sha256=EiAt7dxGTaHuuj7bCNxgAqZbX0i3sldO0mBxOG-aMnY,595
 mdkits/util/.fig_operation.py.swp,sha256=iZYqdYMj4UKS1rmbXv8Ve2FcVBcNljX7Y43-neMdPSk,12288
 mdkits/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mdkits/util/arg_type.py,sha256=o4Fz5VaNBpCWvnJ0u7tKex1sOGx9d2PFtXHmEFMJbA4,2437
+mdkits/util/arg_type.py,sha256=_WmcFKUeOvG5LmQwzcL8-xBQgdwIxUP3gMqEqU7FYNU,2428
 mdkits/util/cp2k_input_parsing.py,sha256=7NMVOYEGycarokLJlhLoWWilciM7sd8MWp5FVTF7hqI,1223
 mdkits/util/encapsulated_ase.py,sha256=uhqIhsALxzwJYuFrfOYGGC6U0QLm_dcZNridvfl_XGc,4339
 mdkits/util/encapsulated_mda.py,sha256=m3i-XrcscMcM5V7JzLnor3JtAOfuDx3LLMl0tZt0n-w,2325
 mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,1045
-mdkits/util/numpy_geo.py,sha256=SUBkR1BsotELTbfSb-OIdheYozPDXGJQgktPlOYz4I4,3724
+mdkits/util/numpy_geo.py,sha256=zkh3uNC3HGHIwtHOmiDXborab5_40PmaJF54jSQ-njU,3874
 mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
 mdkits/util/out_err.py,sha256=7vGDI7wVoJWe1S0BDbcq-UC2KAhblCzg-NAYZKBZ4lo,900
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
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