def GetGdirAngle(coords1, coords2, coords3, r_21=None, r_23=None): """Calculate direction of energy gradients between bond angle atoms. Args: coords1 (float*): 3 cartesian coordinates [Angstrom] of atom1. coords2 (float*): 3 cartesian coordinates [Angstrom] of atom2. coords3 (float*): 3 cartesian coordinates [Angstrom] of atom3. r_21 (float): Distance between atom2 and atom1 (default None). r_23 (float): Distance between atom2 and atom3 (default None). Returns: gdir1 (float*), gdir2 (float*), gdir3 (float*): vectors in the direction of max increasing bond angle. """ if r_21 is not None: r_21 = geomcalc.GetRij(coords2, coords1) if r_23 is not None: r_23 = geomcalc.GetRij(coords2, coords3) u_21 = geomcalc.GetUij(coords2, coords1, r_21) u_23 = geomcalc.GetUij(coords2, coords3, r_23) cp = geomcalc.GetUcp(u_21, u_23) gdir1 = geomcalc.GetUcp(u_21, cp) / r_21 gdir3 = geomcalc.GetUcp(cp, u_23) / r_23 gdir2 = -1.0 * (gdir1 + gdir3) return gdir1, gdir2, gdir3
def GetGDirTorsion(coords1, coords2, coords3, coords4, r_12=None, r_23=None, r_34=None): """Calculate direction of energy gradients between torsion atoms. Args: coords1 (float*): 3 cartesian coordinates [Angstrom] of atom1. coords2 (float*): 3 cartesian coordinates [Angstrom] of atom2. coords3 (float*): 3 cartesian coordinates [Angstrom] of atom3. coords4 (float*): 3 cartesian coordinates [Angstrom] of atom4. r_12 (float): Distance between atom1 and atom2 (default None). r_23 (float): Distance between atom2 and atom3 (default None). r_34 (float): Distance between atom3 and atom4 (default None). Returns: gdir1 (float*), gdir2 (float*), gdir3 (float*), gdir4 (float*): Vectors in the direction of max increasing torsion angle. """ u_21 = geomcalc.GetUij(coords2, coords1, r_12) u_34 = geomcalc.GetUij(coords3, coords4, r_34) u_23 = geomcalc.GetUij(coords2, coords3, r_23) u_32 = -1.0 * u_23 a_123 = geomcalc.GetAijk(coords1, coords2, coords3, r_12, r_23) a_432 = geomcalc.GetAijk(coords4, coords3, coords2, r_34, r_23) s_123 = math.sin(const.DEG2RAD * a_123) s_432 = math.sin(const.DEG2RAD * a_432) c_123 = math.cos(const.DEG2RAD * a_123) c_432 = math.cos(const.DEG2RAD * a_432) gdir1 = geomcalc.GetUcp(u_21, u_23) / (r_12*s_123) gdir4 = geomcalc.GetUcp(u_34, u_32) / (r_34*s_432) gdir2 = (r_12/r_23*c_123 - 1.0)*gdir1 - (r_34/r_23*c_432)*gdir4 gdir3 = (r_34/r_23*c_432 - 1.0)*gdir4 - (r_12/r_23*c_123)*gdir1 return gdir1, gdir2, gdir3, gdir4
def GetGdirOutofplane(coords1, coords2, coords3, coords4, oop, r_31=None, r_32=None, r_34=None): """Calculate direction of energy gradients between outofplane atoms. Args: coords1 (float*): 3 cartesian coordinates [Angstrom] of atom1. coords2 (float*): 3 cartesian coordinates [Angstrom] of atom2. coords3 (float*): 3 cartesian coordinates [Angstrom] of atom3. coords4 (float*): 3 cartesian coordinates [Angstrom] of atom4. oop (float): Out-of-plane angles bewteen atoms 1, 2, 3, and 4. r_31 (float): Distance between atom3 and atom1 (default None). r_32 (float): Distance between atom3 and atom2 (default None). r_34 (float): Distance between atom3 and atom4 (default None). Returns: gdir1 (float*), gdir2 (float*), gdir3 (float*), gdir4 (float*): Vectors in the direction of max increasing outofplane angle. """ if r_31 is not None: r_31 = geomcalc.GetRij(coords3, coords1) if r_32 is not None: r_32 = geomcalc.GetRij(coords3, coords2) if r_34 is not None: r_34 = geomcalc.GetRij(coords3, coords4) u_31 = geomcalc.GetUij(coords3, coords1, r_31) u_32 = geomcalc.GetUij(coords3, coords2, r_32) u_34 = geomcalc.GetUij(coords3, coords4, r_34) cp_3234 = geomcalc.GetCp(u_32, u_34) cp_3431 = geomcalc.GetCp(u_34, u_31) cp_3132 = geomcalc.GetCp(u_31, u_32) a_132 = geomcalc.GetAijk(coords1, coords3, coords2) s_132 = math.sin(const.DEG2RAD * a_132) c_132 = math.cos(const.DEG2RAD * a_132) c_oop = math.cos(const.DEG2RAD * oop) t_oop = math.tan(const.DEG2RAD * oop) gdir1 = ((1.0 / r_31) * (cp_3234 / (c_oop * s_132) - (t_oop / s_132**2) * (u_31 - c_132 * u_32))) gdir2 = ((1.0 / r_32) * (cp_3431 / (c_oop * s_132) - (t_oop / s_132**2) * (u_32 - c_132 * u_31))) gdir4 = ((1.0 / r_34) * (cp_3132 / (c_oop * s_132) - (t_oop * u_34))) gdir3 = -1.0 * (gdir1 + gdir2 + gdir4) return gdir1, gdir2, gdir3, gdir4
def GetEBoundI(k_box, bound, coords, origin, boundtype): """Calculate simulation boundary energy of an atom. Args: k_box (float): Spring constant [kcal/(mol*A^2)] of boundary. bound (float): Distance from origin [Angstrom] of boundary. coords (float*): Array of cartesian coordinates [Angstrom] of atom. origin (float*): Array of cartesian coordiantes [Angstrom] of origin of simulation. boundtype (str): 'cube' or 'sphere', type of boundary condition. Returns: e_bound_i (float): Boundary energy [kcal/mol] of atom. """ e_bound_i = 0.0 if (boundtype == 'cube'): for j in range(const.NUMDIM): scale = 1.0 if (abs(coords[j] - origin[j]) >= bound) else 0.0 e_bound_i += (scale * k_box * (abs(coords[j] - origin[j]) - bound)**2) elif (boundtype == 'sphere'): r_io = geomcalc.GetRij(origin, coords) u_io = geomcalc.GetUij(origin, coords) scale = 1.0 if (r_io >= bound) else 0.0 e_bound_i += scale * k_box * (r_io - bound)**2 return e_bound_i
def GetGBoundI(k_box, bound, coord, origin, boundtype): """Calculate energy gradient magnitude of boundary energy. Args: k_box (float): Spring constant [kcal/(mol*A^2)] of boundary. bound (float): Distance from origin [Angstrom] of boundary. coords (float*): Array of cartesian coordinates [Angstrom] of atom. origin (float*): Array of cartesian coordiantes [Angstrom] of origin of simulation. boundtype (str): 'cube' or 'sphere', type of boundary condition. Returns: g_bound_i (float): Magnitude of energy gradient [kcal/(mol*A)]. """ g_bound_i = numpy.zeros(const.NUMDIM) if boundtype == 'cube': for j in range(const.NUMDIM): sign = 1.0 if (coord[j] - origin[j]) <= 0.0 else -1.0 scale = 1.0 if abs(coord[j] - origin[j]) >= bound else 0.0 g_bound_i[j] = (-2.0 * sign * scale * k_box * (abs(coord[j]) - bound)) elif boundtype == 'sphere': r_io = geomcalc.GetRij(origin, coord) u_io = geomcalc.GetUij(origin, coord) scale = 1.0 if r_io >= bound else 0.0 g_bound_i = 2.0 * scale * k_box * (r_io - bound) * u_io return g_bound_i
def GetGdirInter(coords1, coords2, r_12=None): """Calculate direction of energy gradient between atom pair. Args: coords1 (float*): 3 Cartesian coordinates [Angstrom] of atom1. coords2 (float*): 3 Cartesian coordiantes [Angstrom] of atom2. r_ij (float): Distance between atom1 and atom2 (default None). Returns: gdir1 (float*), gdir2 (float*): unit vectors in the direction of max increasing inter-atomic distance. """ gdir1 = geomcalc.GetUij(coords2, coords1, r_12) gdir2 = -1.0 * gdir1 return gdir1, gdir2
def testAntiReflexive(self): """Asserts opposite value for inverted order of inputs.""" params = ARBITRARY_XYZ2, ARBITRARY_XYZ1 self.assertListAlmostEqual(geomcalc.GetUij(*params), UNIT_VECTOR_21)
def testArbitrary(self): """Asserts correct unit vector between arbitrary points in 3d space.""" params = ARBITRARY_XYZ1, ARBITRARY_XYZ2 self.assertListAlmostEqual(geomcalc.GetUij(*params), UNIT_VECTOR_12)
def testOnAxisZ(self): """Asserts correct on-axis unit vector between points on the z-axis.""" params = POSITIVE_ARBITRARY_Z, NEGATIVE_ARBITRARY_Z self.assertListAlmostEqual(geomcalc.GetUij(*params), NEGATIVE_UNIT_Z)
def testUnitLength(self): """Asserts correct direction for points separated by unit distance.""" params = POSITIVE_UNIT_X, ORIGIN self.assertListAlmostEqual(geomcalc.GetUij(*params), NEGATIVE_UNIT_X)
def testSamePoint(self): """Asserts zero vector between identical points.""" params = ARBITRARY_XYZ1, ARBITRARY_XYZ1 self.assertListAlmostEqual(geomcalc.GetUij(*params), ORIGIN)