Merge branch 'develop' into plumed-plugin
This commit is contained in:
Axel Kohlmeyer
@ -101,6 +101,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(extract_setting);
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ADDSYM(extract_global_datatype);
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ADDSYM(extract_global);
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ADDSYM(extract_pair_dimension);
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ADDSYM(extract_pair);
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ADDSYM(map_atom);
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ADDSYM(extract_atom_datatype);
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@ -144,11 +144,13 @@ struct _liblammpsplugin {
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int (*get_mpi_comm)(void *);
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int (*extract_setting)(void *, const char *);
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int *(*extract_global_datatype)(void *, const char *);
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int (*extract_global_datatype)(void *, const char *);
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void *(*extract_global)(void *, const char *);
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void *(*map_atom)(void *, const void *);
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int (*extract_pair_dimension)(void *, const char *);
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void *(*extract_pair)(void *, const char *);
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int (*map_atom)(void *, const void *);
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int *(*extract_atom_datatype)(void *, const char *);
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int (*extract_atom_datatype)(void *, const char *);
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void *(*extract_atom)(void *, const char *);
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void *(*extract_compute)(void *, const char *, int, int);
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@ -5,9 +5,9 @@ dimension 3
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atom_style full
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processors * * 1
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pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
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pair_style lj/spica/coul/long 15.0
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bond_style harmonic
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angle_style sdk # compatible with "spica"
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angle_style spica
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special_bonds lj/coul 0.0 0.0 1.0
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read_data data.sds.gz
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@ -1,2 +1,3 @@
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*.csv
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*.txt
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*.lammpstrj
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@ -17,14 +17,22 @@ q_ref = float(ref_line[3])
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inv11_ref = float(ref_line[4])
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inv12_ref = float(ref_line[5])
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b1_ref = float(ref_line[6])
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felec1_ref = float(ref_line[8])
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felyt1_ref = float(ref_line[10])
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press_ref = float(ref_line[12])
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# out.csv
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with open(sys.argv[2]) as f:
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out_line = f.readlines()[-1].split(", ")
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e_out = float(out_line[0])
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q_out = float(out_line[1])
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press_out = float(out_line[2])
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out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)]
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out_lines = [
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("energy", e_ref, e_out),
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("charge", q_ref, q_out),
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("pressure", press_ref, press_out),
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]
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# vec.csv
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vec_file = "vec.csv"
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@ -44,6 +52,14 @@ if op.isfile(inv_file):
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inv12_out = float(inv_line[1])
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out_lines.append(("inv11", inv11_ref, inv11_out))
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# forces.lammpstrj
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force_file = "forces.lammpstrj"
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with open(force_file) as f:
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lines = f.readlines()[9:]
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for name, i, f_ref in [("felec1", "1", felec1_ref), ("felyt1", "3", felyt1_ref)]:
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f_out = next(float(y[3]) for x in lines if (y := x.split()) and y[0] == i)
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out_lines.append((name, f_ref, f_out))
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lines = []
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for label, ref, out in out_lines:
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error = rel_error(out, ref)
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@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
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fix feta all property/atom d_eta ghost on
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set group bot d_eta 0.5
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set group top d_eta 3.0
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fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
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fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta algo cg 1e-6
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run 0
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@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
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fix feta all property/atom d_eta ghost on
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set group bot d_eta 0.5
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set group top d_eta 3.0
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fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
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fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
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run 0
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@ -1,12 +1,17 @@
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#!/usr/bin/env python3
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import time
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import numpy as np
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from scipy.special import erf
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SQRT2 = np.sqrt(2)
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SQRTPI_INV = 1 / np.sqrt(np.pi)
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COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units
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QE2F = 23.060549
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NKTV2P = 68568.415 # pressure in 'real' units
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LENGTH = 10000 # convergence parameter
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LZ = 20
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def lattice(length):
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@ -26,6 +31,25 @@ def b_element(r, q, eta):
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return q * erf(eta * r) / r
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def force_gauss(r, qq, eta):
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etar = eta * r
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return (qq / np.square(r)) * (
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erf(etar) - 2 * etar * SQRTPI_INV * np.exp(-np.square(etar))
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)
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def force_point(r, qq):
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return qq / np.square(r)
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def force_component(dx, d, qq, eta=None):
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if eta:
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return np.sum(dx / d * force_gauss(d, qq, eta))
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else:
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return np.sum(dx / d * force_point(d, qq))
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time_start = time.perf_counter()
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a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2)
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x_elec = [-2, 2]
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x_elyt = [-1, 1]
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@ -36,8 +60,20 @@ v = np.array([-0.5, 0.5]) * (QE2F / COULOMB)
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# distances to images within electrode and to opposite electrode
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distances = a * np.linalg.norm(lattice(LENGTH), axis=1)
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opposite_distances = np.sqrt(np.square(distances) + distance_plates**2)
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image_distances = []
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for x in x_elec:
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image_distances.append([])
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for y in x_elyt:
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image_distances[-1].append(np.sqrt(np.square(distances) + np.abs(y - x) ** 2))
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image_elyt_distances = [[None for _ in range(len(x_elyt))] for _ in range(len(x_elyt))]
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for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
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for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
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image_elyt_distances[i][j] = np.sqrt(
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np.square(distances) + np.abs(xj - xi) ** 2
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)
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for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
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# for name, eta_elec in [("", [2.0, 2.0])]:
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eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec)))
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# self interaction and within original box
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A_11 = np.sqrt(2 / np.pi) * eta_elec[0]
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@ -55,22 +91,18 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
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# electrode-electrolyte interaction
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b = []
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for x, eta in zip(x_elec, eta_elec):
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for i, (x, eta) in enumerate(zip(x_elec, eta_elec)):
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bi = 0
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for y, q in zip(x_elyt, q_elyt):
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d = abs(y - x)
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bi += b_element(d, q, eta)
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image_distances = np.sqrt(np.square(distances) + d**2)
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bi += 4 * np.sum(b_element(image_distances, q, eta))
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for j, (y, q) in enumerate(zip(x_elyt, q_elyt)):
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bi += b_element(np.abs(y - x), q, eta)
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bi += 4 * np.sum(b_element(image_distances[i][j], q, eta))
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b.append(bi)
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b = np.array(b)
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# electrolyte-electrolyte energy
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elyt_11 = 4 * np.sum(1 / distances)
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distance_elyt = x_elyt[1] - x_elyt[0]
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elyt_12 = 1 / distance_elyt + 4 * np.sum(
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1 / np.sqrt(np.square(distances) + distance_elyt**2)
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)
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elyt_12 = 1 / distance_elyt + 4 * np.sum(1 / image_elyt_distances[0][1])
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elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
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energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
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@ -78,9 +110,48 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
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q = np.dot(inv, v - b)
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energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
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# forces in out-of-plane direction
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f_elec = np.zeros(len(x_elec))
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f_elyt = np.zeros(len(x_elyt))
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# electrode-electrode
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dx = x_elec[1] - x_elec[0]
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fij_box = force_component(dx, np.abs(dx), q[0] * q[1], eta_mix)
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fij_img = 4 * force_component(dx, opposite_distances, q[0] * q[1], eta_mix)
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f_elec[0] -= fij_box + fij_img
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f_elec[1] += fij_box + fij_img
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# electrode-electrolyte
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for i, (xi, qi, etai) in enumerate(zip(x_elec, q, eta_elec)):
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for j, (xj, qj) in enumerate(zip(x_elyt, q_elyt)):
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dx = xj - xi
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fij_box = force_component(dx, np.abs(dx), qi * qj, etai)
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fij_img = 4 * force_component(dx, image_distances[i][j], qi * qj, etai)
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f_elec[i] -= fij_box + fij_img
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f_elyt[j] += fij_box + fij_img
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# electrolyte-electrolyte
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for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
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for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
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dx = xj - xi
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fij_box = force_component(dx, np.abs(dx), qi * qj)
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fij_img = 4 * force_component(dx, image_elyt_distances[i][j], qi * qj)
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f_elyt[i] -= fij_img + fij_box
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f_elyt[j] += fij_img + fij_box
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# force units
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assert np.abs(np.sum(f_elec) + np.sum(f_elyt)) < 1e-8
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f_elec *= COULOMB
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f_elyt *= COULOMB
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# Virial
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volume = a**2 * LZ
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virial = 0.0
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for x, f in [(x_elec, f_elec), (x_elyt, f_elyt)]:
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virial += np.dot(x, f)
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pressure = NKTV2P * virial / volume
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with open(f"plate_cap{name}.csv", "w") as f:
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f.write(
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"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n"
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"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A"
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+ ", b1 / e/A, b2 / e/A, felec1 / kcal/mol/A, felec2 / kcal/mol/A"
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+ ", felyt1 / kcal/mol/A, felyt2 / kcal/mol/A, press\n"
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)
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f.write(
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", ".join(
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@ -93,7 +164,14 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
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f"{inv[0, 1]:.10f}",
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f"{b[0]:.8f}",
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f"{b[1]:.8f}",
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f"{f_elec[0]:.5f}",
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f"{f_elec[1]:.5f}",
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f"{f_elyt[0]:.5f}",
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f"{f_elyt[1]:.5f}",
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f"{pressure:.2f}",
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]
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)
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+ "\n"
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)
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time_end = time.perf_counter()
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print(f"{time_end - time_start:0.4f} seconds")
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@ -19,4 +19,8 @@ compute qtop top reduce sum v_q
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compute compute_pe all pe
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variable vpe equal c_compute_pe
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variable charge equal c_qtop
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fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
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compute press all pressure NULL virial
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variable p3 equal c_press[3]
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fix fxprint all print 1 "${vpe}, ${charge}, ${p3}" file "out.csv"
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dump dump_forces all custom 1 forces.lammpstrj id fx fy fz
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File diff suppressed because it is too large
Load Diff
@ -42,7 +42,11 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
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||||
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
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||||
fix fxforce_wa wall setforce 0.0 0.0 NULL
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fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
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variable atm equal 1/68568.415 # 1/force->nktv2p
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variable area equal (xhi-xlo)*(yhi-ylo)
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variable wall_force equal -v_atm*v_area/count(wall)
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print "Wall force per atom: ${wall_force}"
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fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
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fix fxdrag wall viscous 100
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fix fxrigid wall rigid/nve single
|
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|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (3 Nov 2022)
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
|
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using 1 OpenMP thread(s) per MPI task
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# The intention is to find the average position of one wall at atmospheric
|
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# pressure. The output is the wall position over time which can be used to
|
||||
# find the average position for a run with fixed wall position.
|
||||
@ -40,8 +41,8 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
1 = max # of 1-3 neighbors
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||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
# ----------------- Settings Section -----------------
|
||||
|
||||
@ -77,7 +78,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
|
||||
|
||||
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
|
||||
fix fxforce_wa wall setforce 0.0 0.0 NULL
|
||||
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
|
||||
variable atm equal 1/68568.415 # 1/force->nktv2p
|
||||
variable area equal (xhi-xlo)*(yhi-ylo)
|
||||
variable wall_force equal -v_atm*v_area/count(wall)
|
||||
print "Wall force per atom: ${wall_force}"
|
||||
Wall force per atom: -0.000109285996244287
|
||||
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
|
||||
fix fxpressure wall aveforce 0 0 -0.000109285996244287
|
||||
fix fxdrag wall viscous 100
|
||||
fix fxrigid wall rigid/nve single
|
||||
1 rigid bodies with 48 atoms
|
||||
@ -134,7 +141,7 @@ PPPM/electrode initialization ...
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.02930901
|
||||
estimated relative force accuracy = 8.8263214e-05
|
||||
using double precision MKL FFT
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 15884 6480
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
@ -157,54 +164,54 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
|
||||
Step c_temp_mobile c_qwa c_qau v_top_wall
|
||||
0 303.38967 -0.042963484 0.042963484 21.4018
|
||||
5000 285.08828 -0.26105255 0.26105255 25.155629
|
||||
10000 323.19176 -0.26264003 0.26264003 24.541676
|
||||
15000 310.479 -0.27318148 0.27318148 23.141522
|
||||
20000 295.18544 -0.11313444 0.11313444 23.828735
|
||||
25000 295.38607 -0.25433086 0.25433086 23.673314
|
||||
30000 288.0613 -0.30099901 0.30099901 23.438086
|
||||
35000 278.5591 -0.15823576 0.15823576 24.311915
|
||||
40000 303.95751 -0.19941381 0.19941381 23.69594
|
||||
45000 279.026 -0.1659962 0.1659962 23.588604
|
||||
50000 298.79278 -0.28866703 0.28866703 23.372508
|
||||
55000 301.03353 -0.078370381 0.078370381 23.192985
|
||||
60000 306.77965 -0.12807205 0.12807205 23.968574
|
||||
65000 309.86008 -0.27162663 0.27162663 23.616704
|
||||
70000 287.31116 -0.029751882 0.029751882 23.667495
|
||||
75000 312.48654 -0.10759866 0.10759866 23.504105
|
||||
80000 309.94267 -0.2558548 0.2558548 23.810576
|
||||
85000 328.04389 -0.1575471 0.1575471 24.013437
|
||||
90000 302.9806 -0.032002164 0.032002164 24.264432
|
||||
95000 294.20804 -0.27797238 0.27797238 23.291758
|
||||
100000 307.63019 -0.19047448 0.19047448 23.632147
|
||||
Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
|
||||
5000 311.85363 0.03543775 -0.03543775 24.79665
|
||||
10000 285.91321 -0.16873703 0.16873703 23.103088
|
||||
15000 295.39476 -0.44424612 0.44424612 23.767107
|
||||
20000 296.12969 -0.14120993 0.14120993 23.96361
|
||||
25000 306.59629 -0.29333182 0.29333182 23.884488
|
||||
30000 297.98559 -0.10749684 0.10749684 23.73316
|
||||
35000 297.98503 -0.11809975 0.11809975 23.984669
|
||||
40000 300.26292 -0.32784184 0.32784184 23.462748
|
||||
45000 295.68441 -0.25940165 0.25940165 23.516403
|
||||
50000 315.12883 -0.36037614 0.36037614 23.627879
|
||||
55000 290.55151 -0.0032838106 0.0032838106 23.684931
|
||||
60000 316.4625 -0.17245368 0.17245368 24.126883
|
||||
65000 296.79343 -0.054061851 0.054061851 23.695094
|
||||
70000 305.99923 -0.11363801 0.11363801 23.55476
|
||||
75000 297.40131 -0.27054153 0.27054153 23.928994
|
||||
80000 306.54811 -0.25409719 0.25409719 23.869448
|
||||
85000 303.95231 -0.17895561 0.17895561 23.658833
|
||||
90000 313.43739 -0.059036514 0.059036514 23.36056
|
||||
95000 290.3077 -0.31394478 0.31394478 23.885538
|
||||
100000 297.5156 -0.30730083 0.30730083 23.511674
|
||||
Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
|
||||
|
||||
Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 190.47 | 190.47 | 190.47 | 0.0 | 35.88
|
||||
Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02
|
||||
Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79
|
||||
Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56
|
||||
Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32
|
||||
Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00
|
||||
Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26
|
||||
Other | | 0.9595 | | | 0.18
|
||||
Pair | 460.91 | 460.91 | 460.91 | 0.0 | 29.06
|
||||
Bond | 0.047873 | 0.047873 | 0.047873 | 0.0 | 0.00
|
||||
Kspace | 341.4 | 341.4 | 341.4 | 0.0 | 21.53
|
||||
Neigh | 52.868 | 52.868 | 52.868 | 0.0 | 3.33
|
||||
Comm | 5.2321 | 5.2321 | 5.2321 | 0.0 | 0.33
|
||||
Output | 0.00099102 | 0.00099102 | 0.00099102 | 0.0 | 0.00
|
||||
Modify | 724.63 | 724.63 | 724.63 | 0.0 | 45.69
|
||||
Other | | 0.9741 | | | 0.06
|
||||
|
||||
Nlocal: 726 ave 726 max 726 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2335 ave 2335 max 2335 min
|
||||
Nghost: 2336 ave 2336 max 2336 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 120271 ave 120271 max 120271 min
|
||||
Neighs: 120321 ave 120321 max 120321 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 120271
|
||||
Ave neighs/atom = 165.66253
|
||||
Total # of neighbors = 120321
|
||||
Ave neighs/atom = 165.7314
|
||||
Ave special neighs/atom = 1.7355372
|
||||
Neighbor list builds = 7722
|
||||
Neighbor list builds = 7670
|
||||
Dangerous builds = 0
|
||||
write_data "data.piston.final"
|
||||
System init for write_data ...
|
||||
@ -213,11 +220,11 @@ PPPM/electrode initialization ...
|
||||
G vector (1/distance) = 0.32814871
|
||||
grid = 12 15 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.029311365
|
||||
estimated relative force accuracy = 8.8270304e-05
|
||||
using double precision MKL FFT
|
||||
estimated absolute RMS force accuracy = 0.029311329
|
||||
estimated relative force accuracy = 8.8270197e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 15884 6480
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
|
||||
Average conjugate gradient steps: 1.981
|
||||
Total wall time: 0:08:50
|
||||
Total wall time: 0:26:26
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (3 Nov 2022)
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# The intention is to find the average position of one wall at atmospheric
|
||||
# pressure. The output is the wall position over time which can be used to
|
||||
# find the average position for a run with fixed wall position.
|
||||
@ -41,8 +42,8 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.017 seconds
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
# ----------------- Settings Section -----------------
|
||||
|
||||
@ -66,7 +67,7 @@ Finding SHAKE clusters ...
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
210 = # of frozen angles
|
||||
find clusters CPU = 0.002 seconds
|
||||
find clusters CPU = 0.000 seconds
|
||||
pair_modify mix arithmetic
|
||||
|
||||
# ----------------- Run Section -----------------
|
||||
@ -78,7 +79,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
|
||||
|
||||
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
|
||||
fix fxforce_wa wall setforce 0.0 0.0 NULL
|
||||
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
|
||||
variable atm equal 1/68568.415 # 1/force->nktv2p
|
||||
variable area equal (xhi-xlo)*(yhi-ylo)
|
||||
variable wall_force equal -v_atm*v_area/count(wall)
|
||||
print "Wall force per atom: ${wall_force}"
|
||||
Wall force per atom: -0.000109285996244287
|
||||
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
|
||||
fix fxpressure wall aveforce 0 0 -0.000109285996244287
|
||||
fix fxdrag wall viscous 100
|
||||
fix fxrigid wall rigid/nve single
|
||||
1 rigid bodies with 48 atoms
|
||||
@ -135,7 +142,7 @@ PPPM/electrode initialization ...
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.02930901
|
||||
estimated relative force accuracy = 8.8263214e-05
|
||||
using double precision MKL FFT
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 8512 2880
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
@ -158,54 +165,54 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes
|
||||
Step c_temp_mobile c_qwa c_qau v_top_wall
|
||||
0 303.38967 -0.042963484 0.042963484 21.4018
|
||||
5000 292.03027 -0.19040435 0.19040435 24.581338
|
||||
10000 309.52764 -0.48308301 0.48308301 23.776985
|
||||
15000 295.00243 -0.16591109 0.16591109 23.672038
|
||||
20000 293.5536 -0.086669084 0.086669084 23.426455
|
||||
25000 303.0079 -0.16488112 0.16488112 23.862966
|
||||
30000 306.31463 -0.23192653 0.23192653 23.819882
|
||||
35000 303.66268 -0.2317907 0.2317907 23.495344
|
||||
40000 301.39435 -0.34661329 0.34661329 23.657835
|
||||
45000 291.61205 -0.30539427 0.30539427 23.437303
|
||||
50000 298.65319 -0.096107034 0.096107034 23.57809
|
||||
55000 282.65069 -0.14943539 0.14943539 23.823728
|
||||
60000 310.64182 -0.17418813 0.17418813 23.286959
|
||||
65000 308.47141 -0.02075662 0.02075662 23.91313
|
||||
70000 292.5186 -0.080163162 0.080163162 23.96283
|
||||
75000 270.13928 -0.029528648 0.029528648 23.488972
|
||||
80000 322.10914 0.030761045 -0.030761045 23.47592
|
||||
85000 310.60347 -0.24069996 0.24069996 23.987091
|
||||
90000 294.35695 -0.070458235 0.070458235 23.397929
|
||||
95000 308.69043 -0.2652581 0.2652581 23.473813
|
||||
100000 318.71883 0.024035956 -0.024035956 23.449863
|
||||
Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms
|
||||
5000 291.6303 -0.1820085 0.1820085 24.641399
|
||||
10000 299.42886 -0.19823095 0.19823095 23.820522
|
||||
15000 288.23071 -0.065261869 0.065261869 23.360845
|
||||
20000 299.4644 -0.042993777 0.042993777 23.987554
|
||||
25000 304.26497 -0.15665293 0.15665293 23.729006
|
||||
30000 292.29674 -0.25142779 0.25142779 23.960725
|
||||
35000 295.57492 -0.01269228 0.01269228 23.445383
|
||||
40000 303.38438 -0.13941727 0.13941727 23.517483
|
||||
45000 302.211 -0.19589892 0.19589892 23.704043
|
||||
50000 281.64939 -0.18057298 0.18057298 23.542137
|
||||
55000 274.90565 -0.15453379 0.15453379 23.734347
|
||||
60000 290.70459 -0.27977436 0.27977436 23.835365
|
||||
65000 293.42241 -0.2454241 0.2454241 23.59269
|
||||
70000 295.20229 -0.041314995 0.041314995 23.73856
|
||||
75000 297.79519 -0.11231755 0.11231755 23.57262
|
||||
80000 285.17858 -0.070796508 0.070796508 23.817135
|
||||
85000 311.71609 -0.068920177 0.068920177 23.861127
|
||||
90000 287.80446 -0.19183387 0.19183387 23.369393
|
||||
95000 309.43345 -0.15238671 0.15238671 23.597792
|
||||
100000 294.12422 -0.14284353 0.14284353 23.526286
|
||||
Loop time of 876.546 on 4 procs for 100000 steps with 726 atoms
|
||||
|
||||
Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s
|
||||
72.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 19.714 ns/day, 1.217 hours/ns, 114.084 timesteps/s, 82.825 katom-step/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85
|
||||
Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02
|
||||
Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87
|
||||
Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18
|
||||
Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38
|
||||
Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00
|
||||
Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44
|
||||
Other | | 1.478 | | | 0.25
|
||||
Pair | 123.63 | 171.23 | 215.73 | 336.6 | 19.53
|
||||
Bond | 0.068261 | 0.075883 | 0.081822 | 1.9 | 0.01
|
||||
Kspace | 187.59 | 231.71 | 279.01 | 287.1 | 26.43
|
||||
Neigh | 29.28 | 29.462 | 29.637 | 2.5 | 3.36
|
||||
Comm | 12.544 | 13.731 | 14.929 | 29.1 | 1.57
|
||||
Output | 0.0010182 | 0.0014585 | 0.0016071 | 0.7 | 0.00
|
||||
Modify | 428.74 | 429.25 | 429.74 | 2.3 | 48.97
|
||||
Other | | 1.092 | | | 0.12
|
||||
|
||||
Nlocal: 181.5 ave 207 max 169 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Nghost: 1961.5 ave 1984 max 1926 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 30051 ave 41646 max 20775 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nlocal: 181.5 ave 195 max 166 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 1955.5 ave 1978 max 1931 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 30343 ave 39847 max 20428 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 120204
|
||||
Ave neighs/atom = 165.57025
|
||||
Total # of neighbors = 121372
|
||||
Ave neighs/atom = 167.17906
|
||||
Ave special neighs/atom = 1.7355372
|
||||
Neighbor list builds = 7663
|
||||
Neighbor list builds = 7698
|
||||
Dangerous builds = 0
|
||||
write_data "data.piston.final"
|
||||
System init for write_data ...
|
||||
@ -214,11 +221,11 @@ PPPM/electrode initialization ...
|
||||
G vector (1/distance) = 0.32814871
|
||||
grid = 12 15 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.029311028
|
||||
estimated relative force accuracy = 8.8269289e-05
|
||||
using double precision MKL FFT
|
||||
estimated absolute RMS force accuracy = 0.029310954
|
||||
estimated relative force accuracy = 8.8269069e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 8512 2880
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
|
||||
Average conjugate gradient steps: 1.982
|
||||
Total wall time: 0:09:50
|
||||
Average conjugate gradient steps: 1.981
|
||||
Total wall time: 0:14:36
|
||||
340
examples/charmmfsw/charmmff.cmap
Normal file
340
examples/charmmfsw/charmmff.cmap
Normal file
@ -0,0 +1,340 @@
|
||||
#CMAP for C NH1 CT1 C NH1 CT1 C NH1; id=1
|
||||
#phi = -180.000000
|
||||
0.130000 0.770000 0.970000 1.250000 2.120000
|
||||
2.720000 2.090000 1.790000 0.780000 -0.690000
|
||||
1.000000 -2.200000 -4.830000 -4.820000 -4.910000
|
||||
-3.590000 -2.770000 -2.780000 -2.450000 -2.350000
|
||||
-2.340000 -1.520000 -0.950000 -0.040000
|
||||
|
||||
#phi = -165.000000
|
||||
-0.130000 1.380000 1.580000 1.870000 2.400000
|
||||
2.490000 2.440000 1.930000 1.090000 0.640000
|
||||
0.260000 -2.800000 -4.010000 -4.140000 -3.420000
|
||||
-2.600000 -2.300000 -1.500000 -1.100000 -0.860000
|
||||
-0.640000 -0.210000 -1.080000 -1.120000
|
||||
|
||||
#phi = -150.000000
|
||||
0.080000 1.420000 1.620000 2.050000 2.650000
|
||||
2.720000 2.320000 1.990000 1.560000 2.460000
|
||||
-0.230000 -1.820000 -2.580000 -3.010000 -2.550000
|
||||
-1.890000 -1.350000 -0.730000 0.070000 -0.230000
|
||||
-0.770000 -1.280000 -1.290000 -0.820000
|
||||
|
||||
#phi = -135.000000
|
||||
0.930000 1.520000 2.240000 2.550000 3.110000
|
||||
2.920000 2.460000 2.190000 2.060000 1.850000
|
||||
0.120000 -1.180000 -2.000000 -2.280000 -1.960000
|
||||
-1.340000 -0.930000 0.020000 0.310000 -0.520000
|
||||
-1.150000 -0.980000 -0.570000 -0.440000
|
||||
|
||||
#phi = -120.000000
|
||||
1.360000 1.960000 2.700000 3.040000 3.700000
|
||||
3.560000 2.640000 2.770000 2.720000 1.630000
|
||||
0.710000 -0.790000 -2.120000 -2.630000 -1.800000
|
||||
-0.430000 -0.060000 0.440000 0.910000 -0.550000
|
||||
-0.970000 -0.860000 -0.250000 0.450000
|
||||
|
||||
#phi = -105.000000
|
||||
2.050000 2.540000 2.820000 3.090000 3.370000
|
||||
3.550000 3.070000 2.900000 2.960000 2.120000
|
||||
0.910000 -0.820000 -2.090000 -2.240000 -1.460000
|
||||
0.210000 0.080000 0.770000 1.040000 -0.120000
|
||||
-0.320000 -0.160000 0.310000 0.730000
|
||||
|
||||
#phi = -90.000000
|
||||
1.450000 2.750000 2.740000 3.160000 3.450000
|
||||
3.340000 3.180000 3.900000 3.340000 2.440000
|
||||
0.910000 -0.610000 -1.510000 -1.620000 -0.960000
|
||||
-0.020000 0.420000 0.910000 0.460000 0.150000
|
||||
-0.070000 0.020000 0.280000 0.750000
|
||||
|
||||
#phi = -75.000000
|
||||
1.380000 3.350000 2.350000 3.060000 3.810000
|
||||
3.700000 3.580000 4.210000 3.540000 1.690000
|
||||
0.100000 -0.680000 -0.120000 -0.430000 -0.600000
|
||||
0.230000 0.420000 0.300000 0.550000 0.190000
|
||||
-0.250000 -0.190000 -0.250000 0.470000
|
||||
|
||||
#phi = -60.000000
|
||||
0.240000 1.230000 1.720000 3.170000 4.210000
|
||||
4.390000 4.280000 3.670000 2.270000 -0.480000
|
||||
-0.410000 -0.040000 -0.360000 -0.820000 -0.170000
|
||||
0.140000 0.270000 0.320000 0.310000 -0.670000
|
||||
-0.950000 -1.530000 -1.480000 -0.200000
|
||||
|
||||
#phi = -45.000000
|
||||
-1.180000 0.080000 2.350000 4.210000 5.380000
|
||||
5.390000 4.380000 2.460000 1.120000 0.110000
|
||||
0.010000 -0.150000 -0.800000 -0.580000 0.080000
|
||||
0.270000 -0.050000 0.380000 0.250000 -0.890000
|
||||
-1.580000 -1.950000 -1.980000 -2.000000
|
||||
|
||||
#phi = -30.000000
|
||||
-1.170000 1.070000 4.180000 6.740000 6.070000
|
||||
4.810000 2.780000 1.320000 0.770000 -0.010000
|
||||
0.280000 -0.710000 1.310000 1.520000 1.920000
|
||||
2.220000 0.190000 0.530000 0.330000 -1.600000
|
||||
-2.850000 -3.550000 -3.280000 -2.660000
|
||||
|
||||
#phi = -15.000000
|
||||
0.290000 5.590000 3.730000 3.220000 3.270000
|
||||
2.520000 1.590000 1.380000 0.860000 0.660000
|
||||
1.620000 0.850000 0.510000 0.740000 1.020000
|
||||
1.620000 -0.340000 0.180000 -0.610000 -2.560000
|
||||
-3.790000 -3.810000 -3.160000 -1.750000
|
||||
|
||||
#phi = 0.000000
|
||||
2.830000 0.790000 0.320000 0.480000 0.630000
|
||||
0.980000 1.240000 1.670000 1.650000 2.520000
|
||||
1.610000 0.780000 0.120000 0.070000 0.120000
|
||||
-1.570000 -1.210000 -1.930000 -2.600000 -3.790000
|
||||
-3.930000 -3.620000 -2.680000 -0.920000
|
||||
|
||||
#phi = 15.000000
|
||||
-0.780000 -1.910000 -2.050000 -1.850000 -1.050000
|
||||
0.180000 1.680000 2.220000 1.360000 2.450000
|
||||
1.440000 0.680000 -0.240000 -0.540000 -0.790000
|
||||
-2.180000 -3.210000 -4.350000 -3.940000 -3.910000
|
||||
-3.460000 -2.770000 1.760000 0.310000
|
||||
|
||||
#phi = 30.000000
|
||||
-2.960000 -3.480000 -3.440000 -2.400000 -1.130000
|
||||
0.340000 1.430000 1.390000 0.970000 2.460000
|
||||
1.520000 0.550000 -0.410000 -1.480000 -3.580000
|
||||
-4.130000 -4.560000 -4.440000 -3.580000 -2.960000
|
||||
-1.960000 -1.070000 -1.600000 -2.450000
|
||||
|
||||
#phi = 45.000000
|
||||
-4.020000 -3.840000 -3.370000 -2.330000 -0.980000
|
||||
0.360000 0.810000 0.750000 0.500000 1.900000
|
||||
0.770000 -0.420000 -3.290000 -3.910000 -4.520000
|
||||
-4.890000 -3.850000 -4.150000 -2.670000 -2.370000
|
||||
-2.860000 -3.420000 -3.670000 -3.600000
|
||||
|
||||
#phi = 60.000000
|
||||
-3.350000 -2.980000 -2.320000 -1.240000 -0.260000
|
||||
0.720000 0.670000 0.440000 2.400000 1.630000
|
||||
-2.010000 -3.310000 -3.990000 -4.530000 -4.850000
|
||||
-3.770000 -3.940000 -3.890000 -2.610000 -3.510000
|
||||
-3.760000 -3.640000 -3.450000 -3.340000
|
||||
|
||||
#phi = 75.000000
|
||||
-2.250000 -1.640000 -1.010000 0.040000 0.640000
|
||||
0.820000 0.520000 -0.010000 -0.370000 -1.190000
|
||||
-2.390000 -3.380000 -4.500000 -5.590000 -5.510000
|
||||
-4.940000 -3.830000 -3.840000 -3.700000 -4.150000
|
||||
-4.170000 -3.730000 -3.740000 -2.620000
|
||||
|
||||
#phi = 90.000000
|
||||
-1.720000 -1.180000 -0.430000 0.280000 0.810000
|
||||
0.800000 0.480000 -0.340000 -0.790000 -1.770000
|
||||
-2.810000 -3.800000 -5.220000 -6.280000 -6.580000
|
||||
-5.640000 -5.060000 -4.020000 -4.150000 -4.470000
|
||||
-4.100000 -3.770000 -3.160000 -2.650000
|
||||
|
||||
#phi = 105.000000
|
||||
-1.850000 -1.090000 -0.450000 0.130000 1.010000
|
||||
0.880000 0.490000 -0.220000 -0.860000 -1.680000
|
||||
-3.010000 -4.130000 -5.990000 -6.860000 -6.830000
|
||||
-5.850000 -3.860000 -4.860000 -4.910000 -4.720000
|
||||
-4.600000 -4.090000 -3.270000 -2.410000
|
||||
|
||||
#phi = 120.000000
|
||||
-1.970000 -1.120000 -0.540000 -0.150000 0.760000
|
||||
1.040000 0.760000 0.310000 -0.330000 -1.870000
|
||||
-3.370000 -5.010000 -6.120000 -7.050000 -6.980000
|
||||
-3.700000 -4.510000 -5.090000 -5.420000 -4.850000
|
||||
-4.440000 -4.000000 -3.420000 -2.750000
|
||||
|
||||
#phi = 135.000000
|
||||
-2.110000 -1.170000 -0.320000 -0.010000 0.320000
|
||||
1.090000 0.940000 0.630000 -0.170000 -1.830000
|
||||
-3.470000 -4.950000 -6.110000 -1.920000 -4.050000
|
||||
-5.000000 -5.000000 -4.840000 -4.890000 -4.300000
|
||||
-4.490000 -4.440000 -4.160000 -3.180000
|
||||
|
||||
#phi = 150.000000
|
||||
-1.760000 -0.400000 0.020000 0.360000 0.630000
|
||||
1.260000 1.360000 0.950000 -0.070000 -1.480000
|
||||
-3.150000 1.840000 -1.760000 -5.090000 -5.740000
|
||||
-5.390000 -4.780000 -4.190000 -4.120000 -4.040000
|
||||
-4.130000 -4.030000 -4.030000 -2.940000
|
||||
|
||||
#phi = 165.000000
|
||||
-0.810000 -0.070000 0.380000 0.540000 1.280000
|
||||
1.640000 1.700000 1.520000 0.630000 -1.090000
|
||||
-2.740000 -0.740000 -4.560000 -6.410000 -5.890000
|
||||
-5.140000 -4.190000 -3.670000 -3.840000 -3.560000
|
||||
-3.550000 -3.250000 -2.750000 -1.810000
|
||||
|
||||
|
||||
#CMAP for C NH1 CT2 C NH1 CT2 C NH1; id=2
|
||||
#phi = -180.000000
|
||||
0.235350 0.182300 0.177200 0.396800 0.859400
|
||||
1.489700 2.092500 2.297700 1.808600 0.696200
|
||||
-0.563300 -1.432700 -1.015100 1.426300 -0.564300
|
||||
0.696200 1.808200 2.301700 2.092600 1.489100
|
||||
0.859500 0.396900 0.176900 0.182400
|
||||
|
||||
#phi = -165.000000
|
||||
0.020100 -0.203800 -0.269700 0.014200 0.620800
|
||||
1.392400 2.046200 2.188200 1.683900 0.688500
|
||||
-0.373700 -0.703500 0.837800 3.704000 -0.730100
|
||||
0.594100 1.713100 2.205800 2.026400 1.529800
|
||||
1.027400 0.623800 0.348400 0.182800
|
||||
|
||||
#phi = -150.000000
|
||||
-0.533600 -0.807400 -0.804600 -0.379800 0.365300
|
||||
1.168000 1.641000 1.618100 1.302200 0.615100
|
||||
0.065700 0.738500 2.959500 -2.036600 -0.934600
|
||||
0.407900 1.517000 1.984800 1.833100 1.435200
|
||||
0.995600 0.562200 0.150600 -0.209000
|
||||
|
||||
#phi = -135.000000
|
||||
-1.208500 -1.429400 -1.319200 -0.817500 -0.112400
|
||||
0.454400 0.737600 0.879300 0.850100 0.670300
|
||||
0.943500 -2.651200 -2.829400 -2.199100 -1.065700
|
||||
0.279600 1.322000 1.668300 1.521300 1.193900
|
||||
0.765300 0.246000 -0.315500 -0.823200
|
||||
|
||||
#phi = -120.000000
|
||||
-1.789100 -1.965500 -1.860700 -1.447900 -0.896500
|
||||
-0.401000 -0.015100 0.321300 0.634600 0.976300
|
||||
-1.977500 -2.883200 -2.848500 -2.137900 -0.960300
|
||||
0.308700 1.098100 1.245300 1.133600 0.881800
|
||||
0.448200 -0.153900 -0.823700 -1.404300
|
||||
|
||||
#phi = -105.000000
|
||||
-2.246700 -2.487000 -2.473700 -2.135600 -1.577700
|
||||
-0.980600 -0.429100 0.144700 0.734000 -0.918300
|
||||
-2.299200 -2.882200 -2.668600 -1.847100 -0.719800
|
||||
0.107000 0.496000 0.553500 0.584300 0.494000
|
||||
0.098300 -0.529800 -1.237900 -1.840100
|
||||
|
||||
#phi = -90.000000
|
||||
-2.851100 -3.181100 -3.199500 -2.785300 -2.054300
|
||||
-1.242900 -0.476500 0.288100 -0.045300 -1.470600
|
||||
-2.558800 -2.869400 -2.450300 -1.582200 -0.930800
|
||||
-0.426400 -0.022700 0.000000 -0.097400 -0.136100
|
||||
-0.439600 -1.038600 -1.741000 -2.373200
|
||||
|
||||
#phi = -75.000000
|
||||
-3.961800 -4.268200 -4.109000 -3.364700 -2.252200
|
||||
-1.140400 -0.209800 0.487300 -0.746200 -2.127700
|
||||
-2.932100 -2.898500 -2.247900 -1.730400 -1.177200
|
||||
-0.448200 0.034900 -0.073300 -0.531600 -0.933300
|
||||
-1.360700 -2.009200 -2.745700 -3.424900
|
||||
|
||||
#phi = -60.000000
|
||||
-5.408000 -5.355100 -4.640100 -3.283200 -1.710200
|
||||
-0.423800 0.354400 -0.103700 -1.577700 -2.828300
|
||||
-3.151200 -2.649200 -2.183000 -1.761200 -0.981700
|
||||
-0.174700 0.262600 0.039200 -0.663000 -1.530700
|
||||
-2.478200 -3.465600 -4.334200 -5.011200
|
||||
|
||||
#phi = -45.000000
|
||||
-6.093200 -5.298400 -3.816620 -1.922530 -0.196160
|
||||
0.768200 0.568500 -0.831300 -2.343900 -3.037100
|
||||
-2.663700 -2.191100 -2.022900 -1.438500 -0.649000
|
||||
0.077000 0.441500 0.257500 -0.491100 -1.820600
|
||||
-3.473100 -4.895200 -5.790700 -6.205900
|
||||
|
||||
#phi = -30.000000
|
||||
-5.258225 -3.675795 -1.631110 0.430085 1.496470
|
||||
0.318200 -0.555100 -1.695500 -2.434200 -2.192600
|
||||
-1.691300 -1.890000 -1.708500 -1.206300 -0.567400
|
||||
0.054300 0.497200 0.599600 -0.171000 -2.137600
|
||||
-4.237000 -5.584100 -6.135100 -6.067000
|
||||
|
||||
#phi = -15.000000
|
||||
-3.161820 -0.902080 1.432450 -1.452885 -1.560780
|
||||
-1.665600 -1.783100 -1.755100 -1.329300 -0.731100
|
||||
-1.317000 -1.662800 -1.601200 -1.294900 -0.817300
|
||||
-0.197100 0.549500 0.850400 -0.689700 -2.819900
|
||||
-4.393000 -5.111500 -5.205690 -4.654785
|
||||
|
||||
#phi = 0.000000
|
||||
0.034035 -2.349860 -3.412065 -3.620070 -3.450950
|
||||
-2.875650 -1.787800 -0.541250 0.410450 -0.372500
|
||||
-1.126850 -1.498450 -1.608700 -1.498450 -1.126850
|
||||
-0.372500 0.410450 -0.541250 -1.787800 -2.875650
|
||||
-3.450950 -3.620070 -3.412065 -2.349860
|
||||
|
||||
#phi = 15.000000
|
||||
-3.162345 -4.654785 -5.205690 -5.111500 -4.393000
|
||||
-2.819900 -0.689700 0.850400 0.549500 -0.197100
|
||||
-0.817300 -1.294900 -1.601200 -1.662800 -1.317000
|
||||
-0.731100 -1.329300 -1.755100 -1.783100 -1.665600
|
||||
-1.560780 -1.452885 1.432450 -0.902080
|
||||
|
||||
#phi = 30.000000
|
||||
-5.258220 -6.067000 -6.135100 -5.584100 -4.237000
|
||||
-2.137600 -0.171000 0.599600 0.497200 0.054300
|
||||
-0.567400 -1.206300 -1.708500 -1.890000 -1.691300
|
||||
-2.192600 -2.434200 -1.695500 -0.555100 0.318200
|
||||
1.496470 0.430085 -1.631110 -3.675795
|
||||
|
||||
#phi = 45.000000
|
||||
-6.093300 -6.205900 -5.790700 -4.895200 -3.473100
|
||||
-1.820600 -0.491100 0.257500 0.441500 0.077000
|
||||
-0.649000 -1.438500 -2.022900 -2.191100 -2.663700
|
||||
-3.037100 -2.343900 -0.831300 0.568500 0.768200
|
||||
-0.196160 -1.922530 -3.816620 -5.298400
|
||||
|
||||
#phi = 60.000000
|
||||
-5.407500 -5.011200 -4.334200 -3.465600 -2.478200
|
||||
-1.530700 -0.663000 0.039200 0.262600 -0.174700
|
||||
-0.981700 -1.761200 -2.183000 -2.649200 -3.151200
|
||||
-2.828300 -1.577700 -0.103700 0.354400 -0.423800
|
||||
-1.710200 -3.283200 -4.640100 -5.355100
|
||||
|
||||
#phi = 75.000000
|
||||
-3.961900 -3.424900 -2.745700 -2.009200 -1.360700
|
||||
-0.933300 -0.531600 -0.073300 0.034900 -0.448200
|
||||
-1.177200 -1.730400 -2.247900 -2.898500 -2.932100
|
||||
-2.127700 -0.746200 0.487300 -0.209800 -1.140400
|
||||
-2.252200 -3.364700 -4.109000 -4.268200
|
||||
|
||||
#phi = 90.000000
|
||||
-2.854500 -2.373200 -1.741000 -1.038600 -0.439600
|
||||
-0.136100 -0.097400 0.000000 -0.022700 -0.426400
|
||||
-0.930800 -1.582200 -2.450300 -2.869400 -2.558800
|
||||
-1.470600 -0.045300 0.288100 -0.476500 -1.242900
|
||||
-2.054300 -2.785300 -3.199500 -3.181100
|
||||
|
||||
#phi = 105.000000
|
||||
-2.246400 -1.840100 -1.237900 -0.529800 0.098300
|
||||
0.494000 0.584300 0.553500 0.496000 0.107000
|
||||
-0.719800 -1.847100 -2.668600 -2.882200 -2.299200
|
||||
-0.918300 0.734000 0.144700 -0.429100 -0.980600
|
||||
-1.577700 -2.135600 -2.473700 -2.487000
|
||||
|
||||
#phi = 120.000000
|
||||
-1.788800 -1.404300 -0.823700 -0.153900 0.448200
|
||||
0.881800 1.133600 1.245300 1.098100 0.308700
|
||||
-0.960300 -2.137900 -2.848500 -2.883200 -1.977500
|
||||
0.976300 0.634600 0.321300 -0.015100 -0.401000
|
||||
-0.896500 -1.447900 -1.860700 -1.965500
|
||||
|
||||
#phi = 135.000000
|
||||
-1.208900 -0.823200 -0.315500 0.246000 0.765300
|
||||
1.193900 1.521300 1.668300 1.322000 0.279600
|
||||
-1.065700 -2.199100 -2.829400 -2.651200 0.943500
|
||||
0.670300 0.850100 0.879300 0.737600 0.454400
|
||||
-0.112400 -0.817500 -1.319200 -1.429400
|
||||
|
||||
#phi = 150.000000
|
||||
-0.533400 -0.209000 0.150600 0.562200 0.995600
|
||||
1.435200 1.833100 1.984800 1.517000 0.407900
|
||||
-0.934600 -2.036600 2.959500 0.738500 0.065700
|
||||
0.615100 1.302200 1.618100 1.641000 1.168000
|
||||
0.365300 -0.379800 -0.804600 -0.807400
|
||||
|
||||
#phi = 165.000000
|
||||
0.019900 0.182800 0.348400 0.623800 1.027400
|
||||
1.529800 2.026400 2.205800 1.713100 0.594100
|
||||
-0.730100 3.704000 0.837800 -0.703500 -0.373700
|
||||
0.688500 1.683900 2.188200 2.046200 1.392400
|
||||
0.620800 0.014200 -0.269700 -0.203800
|
||||
|
||||
|
||||
BIN
examples/charmmfsw/data.charmmfsw.gz
Normal file
BIN
examples/charmmfsw/data.charmmfsw.gz
Normal file
Binary file not shown.
46
examples/charmmfsw/in.charmmfsw
Normal file
46
examples/charmmfsw/in.charmmfsw
Normal file
@ -0,0 +1,46 @@
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
# for visualization with LAMMPS-GUI
|
||||
group water type 18 60
|
||||
group nowater subtract all water
|
||||
group ions type 63 64
|
||||
group other subtract all water ions
|
||||
|
||||
# dump viz other image 10 myimage-*.ppm element type size 800 800 zoom 2.82954 shiny 0.5 fsaa yes bond none none view 20 10 box no 0.0 axes no 0.0 0.0 center s 0.521318 0.489856 0.489856
|
||||
# dump_modify viz pad 9 boxcolor darkblue backcolor darkgray element H H H H H H H H H H H H H H H H H H C C C C C C C C C C C C C C C C C C C N N N N N N N N N N N N N N O O O O O O O O O P S Cl K adiam 1 1.92 adiam 2 1.92 adiam 3 1.92 adiam 4 1.92 adiam 5 1.92 adiam 6 1.92 adiam 7 1.92 adiam 8 1.92 adiam 9 1.92 adiam 10 1.92 adiam 11 1.92 adiam 12 1.92 adiam 13 1.92 adiam 14 1.92 adiam 15 1.92 adiam 16 1.92 adiam 17 1.92 adiam 18 1.92 adiam 19 2.72 adiam 20 2.72 adiam 21 2.72 adiam 22 2.72 adiam 23 2.72 adiam 24 2.72 adiam 25 2.72 adiam 26 2.72 adiam 27 2.72 adiam 28 2.72 adiam 29 2.72 adiam 30 2.72 adiam 31 2.72 adiam 32 2.72 adiam 33 2.72 adiam 34 2.72 adiam 35 2.72 adiam 36 2.72 adiam 37 2.72 adiam 38 2.48 adiam 39 2.48 adiam 40 2.48 adiam 41 2.48 adiam 42 2.48 adiam 43 2.48 adiam 44 2.48 adiam 45 2.48 adiam 46 2.48 adiam 47 2.48 adiam 48 2.48 adiam 49 2.48 adiam 50 2.48 adiam 51 2.48 adiam 52 2.432 adiam 53 2.432 adiam 54 2.432 adiam 55 2.432 adiam 56 2.432 adiam 57 2.432 adiam 58 2.432 adiam 59 2.432 adiam 60 2.432 adiam 61 2.88 adiam 62 2.88 adiam 63 3.632 adiam 64 2.816
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.1
Normal file
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.1
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
Reading CMAP parameters from: charmmff.cmap
|
||||
Read in CMAP data for 2 crossterm types
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
Reading data file ...
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10245 atoms
|
||||
reading velocities ...
|
||||
10245 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
15 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
48 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
6973 bonds
|
||||
reading angles ...
|
||||
4057 angles
|
||||
reading dihedrals ...
|
||||
1363 dihedrals
|
||||
reading impropers ...
|
||||
70 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.072 seconds
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
Finding SHAKE clusters ...
|
||||
75 = # of size 2 clusters
|
||||
47 = # of size 3 clusters
|
||||
9 = # of size 4 clusters
|
||||
3265 = # of frozen angles
|
||||
find clusters CPU = 0.003 seconds
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.27938162
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00036407395
|
||||
estimated relative force accuracy = 1.0963718e-06
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 226981 157464
|
||||
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 2 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmmfsw/coul/long, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 16 1.09 1.38032e-07 6
|
||||
Bond: 18 1.09 1.00046e-07 3
|
||||
Bond: 34 1.111 1.11388e-06 10
|
||||
Bond: 39 1.111 4.83041e-08 5
|
||||
Bond: 43 1.111 1.97842e-07 10
|
||||
Bond: 44 1.111 1.71815e-06 10
|
||||
Bond: 59 1.111 8.42509e-08 2
|
||||
Bond: 62 1.111 2.84854e-08 2
|
||||
Bond: 63 1.111 2.14153e-07 46
|
||||
Bond: 64 1.111 1.59305e-07 18
|
||||
Bond: 65 1.08 5.67061e-07 16
|
||||
Bond: 66 1.08 1.43965e-06 4
|
||||
Bond: 67 1 1.81926e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 1.34571e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 2.71955e-07 6530
|
||||
Bond: 75 1 1.46045e-07 10
|
||||
Bond: 79 0.997 5.24499e-07 17
|
||||
Bond: 81 1 1.32984e-07 4
|
||||
Bond: 84 1.04 7.65389e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 5.75241e-07 2
|
||||
Bond: 97 1.325 4.3613e-08 3
|
||||
Angle: 142 104.52 2.67611e-05 3265
|
||||
Per MPI rank memory allocation (min/avg/max) = 143.6 | 143.6 | 143.6 Mbytes
|
||||
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
|
||||
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
|
||||
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
|
||||
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
|
||||
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
|
||||
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
|
||||
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
|
||||
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
|
||||
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2031
|
||||
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
|
||||
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 16 1.09 3.78281e-07 6
|
||||
Bond: 18 1.09 1.12288e-07 3
|
||||
Bond: 34 1.111 7.60709e-07 10
|
||||
Bond: 39 1.111 2.37855e-07 5
|
||||
Bond: 43 1.111 6.00872e-07 10
|
||||
Bond: 44 1.111 3.75324e-07 10
|
||||
Bond: 59 1.111 1.12311e-07 2
|
||||
Bond: 62 1.111 2.99471e-07 2
|
||||
Bond: 63 1.111 6.10589e-07 46
|
||||
Bond: 64 1.111 4.50733e-07 18
|
||||
Bond: 65 1.08 2.90668e-07 16
|
||||
Bond: 66 1.08 1.61592e-07 4
|
||||
Bond: 67 1 5.4508e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 4.1398e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 1.76706e-06 6530
|
||||
Bond: 75 1 3.96686e-07 10
|
||||
Bond: 79 0.997 7.72922e-07 17
|
||||
Bond: 81 1 1.30673e-07 4
|
||||
Bond: 84 1.04 1.44551e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 1.03526e-07 2
|
||||
Bond: 97 1.325 3.64689e-08 3
|
||||
Angle: 142 104.52 0.000130126 3265
|
||||
100 -27913.241 3159.0677 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
|
||||
Loop time of 11.5304 on 1 procs for 100 steps with 10245 atoms
|
||||
|
||||
Performance: 1.499 ns/day, 16.014 hours/ns, 8.673 timesteps/s, 88.852 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.6772 | 8.6772 | 8.6772 | 0.0 | 75.25
|
||||
Bond | 0.012444 | 0.012444 | 0.012444 | 0.0 | 0.11
|
||||
Kspace | 1.2286 | 1.2286 | 1.2286 | 0.0 | 10.66
|
||||
Neigh | 1.5276 | 1.5276 | 1.5276 | 0.0 | 13.25
|
||||
Comm | 0.010441 | 0.010441 | 0.010441 | 0.0 | 0.09
|
||||
Output | 0.00055001 | 0.00055001 | 0.00055001 | 0.0 | 0.00
|
||||
Modify | 0.07101 | 0.07101 | 0.07101 | 0.0 | 0.62
|
||||
Other | | 0.002628 | | | 0.02
|
||||
|
||||
Nlocal: 10245 ave 10245 max 10245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 30479 ave 30479 max 30479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7.05928e+06 ave 7.05928e+06 max 7.05928e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7059275
|
||||
Ave neighs/atom = 689.04588
|
||||
Ave special neighs/atom = 2.3664226
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:11
|
||||
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.4
Normal file
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.4
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
Reading CMAP parameters from: charmmff.cmap
|
||||
Read in CMAP data for 2 crossterm types
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
Reading data file ...
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10245 atoms
|
||||
reading velocities ...
|
||||
10245 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
15 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
48 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
6973 bonds
|
||||
reading angles ...
|
||||
4057 angles
|
||||
reading dihedrals ...
|
||||
1363 dihedrals
|
||||
reading impropers ...
|
||||
70 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.068 seconds
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
Finding SHAKE clusters ...
|
||||
75 = # of size 2 clusters
|
||||
47 = # of size 3 clusters
|
||||
9 = # of size 4 clusters
|
||||
3265 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.27938162
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00036407395
|
||||
estimated relative force accuracy = 1.0963718e-06
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 70516 40824
|
||||
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 2 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmmfsw/coul/long, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 16 1.09 1.38032e-07 6
|
||||
Bond: 18 1.09 1.00046e-07 3
|
||||
Bond: 34 1.111 1.11388e-06 10
|
||||
Bond: 39 1.111 4.83041e-08 5
|
||||
Bond: 43 1.111 1.97842e-07 10
|
||||
Bond: 44 1.111 1.71815e-06 10
|
||||
Bond: 59 1.111 8.42509e-08 2
|
||||
Bond: 62 1.111 2.84854e-08 2
|
||||
Bond: 63 1.111 2.14153e-07 46
|
||||
Bond: 64 1.111 1.59305e-07 18
|
||||
Bond: 65 1.08 5.67061e-07 16
|
||||
Bond: 66 1.08 1.43965e-06 4
|
||||
Bond: 67 1 1.81926e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 1.34571e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 2.71955e-07 6530
|
||||
Bond: 75 1 1.46045e-07 10
|
||||
Bond: 79 0.997 5.24499e-07 17
|
||||
Bond: 81 1 1.32984e-07 4
|
||||
Bond: 84 1.04 7.65389e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 5.75241e-07 2
|
||||
Bond: 97 1.325 4.3613e-08 3
|
||||
Angle: 142 104.52 2.67611e-05 3265
|
||||
Per MPI rank memory allocation (min/avg/max) = 76.88 | 77.06 | 77.25 Mbytes
|
||||
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
|
||||
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
|
||||
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
|
||||
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
|
||||
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
|
||||
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
|
||||
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
|
||||
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
|
||||
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2032
|
||||
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
|
||||
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 16 1.09 3.78281e-07 6
|
||||
Bond: 18 1.09 1.12288e-07 3
|
||||
Bond: 34 1.111 7.60709e-07 10
|
||||
Bond: 39 1.111 2.37855e-07 5
|
||||
Bond: 43 1.111 6.00872e-07 10
|
||||
Bond: 44 1.111 3.75324e-07 10
|
||||
Bond: 59 1.111 1.12311e-07 2
|
||||
Bond: 62 1.111 2.99471e-07 2
|
||||
Bond: 63 1.111 6.10589e-07 46
|
||||
Bond: 64 1.111 4.50733e-07 18
|
||||
Bond: 65 1.08 2.90668e-07 16
|
||||
Bond: 66 1.08 1.61592e-07 4
|
||||
Bond: 67 1 5.4508e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 4.1398e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 1.76706e-06 6530
|
||||
Bond: 75 1 3.96686e-07 10
|
||||
Bond: 79 0.997 7.72922e-07 17
|
||||
Bond: 81 1 1.30673e-07 4
|
||||
Bond: 84 1.04 1.44551e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 1.03526e-07 2
|
||||
Bond: 97 1.325 3.64689e-08 3
|
||||
Angle: 142 104.52 0.000130126 3265
|
||||
100 -27913.241 3159.0676 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
|
||||
Loop time of 3.49837 on 4 procs for 100 steps with 10245 atoms
|
||||
|
||||
Performance: 4.939 ns/day, 4.859 hours/ns, 28.585 timesteps/s, 292.851 katom-step/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.4572 | 2.5133 | 2.5634 | 2.6 | 71.84
|
||||
Bond | 0.0040264 | 0.0050718 | 0.0069286 | 1.6 | 0.14
|
||||
Kspace | 0.45979 | 0.50903 | 0.56364 | 5.6 | 14.55
|
||||
Neigh | 0.42029 | 0.42034 | 0.42036 | 0.0 | 12.02
|
||||
Comm | 0.013207 | 0.013292 | 0.013404 | 0.1 | 0.38
|
||||
Output | 0.00026525 | 0.00029549 | 0.00038249 | 0.0 | 0.01
|
||||
Modify | 0.035024 | 0.035546 | 0.03621 | 0.3 | 1.02
|
||||
Other | | 0.001504 | | | 0.04
|
||||
|
||||
Nlocal: 2561.25 ave 2599 max 2520 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 16491.5 ave 16541 max 16442 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1.99855e+06 ave 2.04035e+06 max 1.95468e+06 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 7994217
|
||||
Ave neighs/atom = 780.30425
|
||||
Ave special neighs/atom = 2.3664226
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
75
examples/rheo/balloon/in.rheo.balloon
Normal file
75
examples/rheo/balloon/in.rheo.balloon
Normal file
@ -0,0 +1,75 @@
|
||||
# ------ 2D water balloon ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -40 40 0 80 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
|
||||
region fluid sphere -10 40 0 30 units box side in
|
||||
lattice hex 1.0
|
||||
create_atoms 1 region fluid
|
||||
|
||||
region shell sphere -10 40 0 27 units box side out
|
||||
group shell region shell
|
||||
|
||||
set group shell rheo/status 1
|
||||
set group all vx 0.005 vy -0.04
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
create_bonds many shell shell 1 0 1.5
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# A lower critical strain allows the balloon to pop
|
||||
#bond_coeff 1 1.0 0.05 1.0
|
||||
|
||||
# ------ Drop balloon ------#
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||
run 30000
|
||||
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
@ -0,0 +1,382 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D water balloon ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -40 40 0 80 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
Created orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region fluid sphere -10 40 0 30 units box side in
|
||||
lattice hex 1.0
|
||||
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||
create_atoms 1 region fluid
|
||||
Created 2830 atoms
|
||||
using lattice units in orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
region shell sphere -10 40 0 27 units box side out
|
||||
group shell region shell
|
||||
544 atoms in group shell
|
||||
|
||||
set group shell rheo/status 1
|
||||
Setting atom values ...
|
||||
544 settings made for rheo/status
|
||||
set group all vx 0.005 vy -0.04
|
||||
Setting atom values ...
|
||||
2830 settings made for vx
|
||||
2830 settings made for vy
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable kappa equal 0.01*1/${mp}
|
||||
variable kappa equal 0.01*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
create_bonds many shell shell 1 0 1.5
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 49 49 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair rheo, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) pair rheo/solid, perpetual, trim from (2)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Added 1263 bonds, new total = 1263
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
6 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# A lower critical strain allows the balloon to pop
|
||||
#bond_coeff 1 1.0 0.05 1.0
|
||||
|
||||
# ------ Drop balloon ------#
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||
run 30000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 49 49 1
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (1)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.63 | 17.64 | 17.65 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0.0008125 0.00035927734 2830
|
||||
200 20 0.0008125 0.00035927734 2830
|
||||
400 40 0.0008125 0.00035927734 2830
|
||||
600 60 0.0008125 0.00035927734 2830
|
||||
800 80 0.0008125 0.00035927734 2830
|
||||
1000 100 0.0008125 0.00035927734 2830
|
||||
1200 120 0.0008125 0.00035927734 2830
|
||||
1400 140 0.0008125 0.00035927734 2830
|
||||
1600 160 0.0008125 0.00035927734 2830
|
||||
1800 180 0.0008125 0.00035927734 2830
|
||||
2000 200 0.0008125 0.00035927734 2830
|
||||
2200 220 0.0008125 0.00035927734 2830
|
||||
2400 240 0.00079033569 0.00043037861 2830
|
||||
2600 260 0.0007549229 0.00045188383 2830
|
||||
2800 280 0.00072808836 0.00031695003 2830
|
||||
3000 300 0.0007017958 1.6121754e-05 2830
|
||||
3200 320 0.00067479047 -0.00015725514 2830
|
||||
3400 340 0.00064762254 -0.00023361314 2830
|
||||
3600 360 0.00061960255 -0.00033837679 2830
|
||||
3800 380 0.0005857206 -0.00051770716 2830
|
||||
4000 400 0.00055061733 -0.00070309251 2830
|
||||
4200 420 0.00051884719 -0.0008247795 2830
|
||||
4400 440 0.00049022236 -0.00099918413 2830
|
||||
4600 460 0.00046060011 -0.0010923159 2830
|
||||
4800 480 0.00042900173 -0.0011524571 2830
|
||||
5000 500 0.00039751503 -0.0012586358 2830
|
||||
5200 520 0.00036620054 -0.0013973543 2830
|
||||
5400 540 0.00033130023 -0.0015185231 2830
|
||||
5600 560 0.00030565892 -0.0016159836 2830
|
||||
5800 580 0.00028209836 -0.0016925198 2830
|
||||
6000 600 0.00024695044 -0.0017796892 2830
|
||||
6200 620 0.00021190635 -0.0018706272 2830
|
||||
6400 640 0.0001947093 -0.0019146643 2830
|
||||
6600 660 0.00018903936 -0.0019146199 2830
|
||||
6800 680 0.00017753371 -0.0019390155 2830
|
||||
7000 700 0.00015170593 -0.0020247472 2830
|
||||
7200 720 0.00011509692 -0.0021222209 2830
|
||||
7400 740 7.9861785e-05 -0.0022033181 2830
|
||||
7600 760 6.1350463e-05 -0.0022511971 2830
|
||||
7800 780 6.5269523e-05 -0.0022222806 2830
|
||||
8000 800 8.5709569e-05 -0.0021089664 2830
|
||||
8200 820 0.00011746348 -0.0019351493 2830
|
||||
8400 840 0.00015698134 -0.0017079928 2830
|
||||
8600 860 0.00019758065 -0.0014618965 2830
|
||||
8800 880 0.00023338199 -0.0012365832 2830
|
||||
9000 900 0.00026282353 -0.0010348527 2830
|
||||
9200 920 0.00028604776 -0.00085287884 2830
|
||||
9400 940 0.00030388767 -0.000681122 2830
|
||||
9600 960 0.000317589 -0.00052203521 2830
|
||||
9800 980 0.00032716728 -0.00037501187 2830
|
||||
10000 1000 0.00033270692 -0.00025576132 2830
|
||||
10200 1020 0.00033485986 -0.00016554207 2830
|
||||
10400 1040 0.00033476763 -9.8525417e-05 2830
|
||||
10600 1060 0.00033351922 -5.1166347e-05 2830
|
||||
10800 1080 0.00033161645 -2.0773965e-05 2830
|
||||
11000 1100 0.00032913022 2.2384421e-07 2830
|
||||
11200 1120 0.00032618376 1.2304773e-05 2830
|
||||
11400 1140 0.00032310409 1.3725982e-05 2830
|
||||
11600 1160 0.0003202128 9.0431945e-06 2830
|
||||
11800 1180 0.00031760386 -5.3537879e-07 2830
|
||||
12000 1200 0.00031518884 -1.331708e-05 2830
|
||||
12200 1220 0.00031283958 -3.0838612e-05 2830
|
||||
12400 1240 0.0003104901 -5.0038548e-05 2830
|
||||
12600 1260 0.00030811597 -6.9699925e-05 2830
|
||||
12800 1280 0.00030555782 -8.9972287e-05 2830
|
||||
13000 1300 0.00030256671 -0.00011712941 2830
|
||||
13200 1320 0.00029907961 -0.00015495826 2830
|
||||
13400 1340 0.00029504656 -0.00020292633 2830
|
||||
13600 1360 0.0002905184 -0.00024892421 2830
|
||||
13800 1380 0.00028564542 -0.000295085 2830
|
||||
14000 1400 0.00028073246 -0.00034571956 2830
|
||||
14200 1420 0.00027611457 -0.00039341977 2830
|
||||
14400 1440 0.00027217382 -0.0004281012 2830
|
||||
14600 1460 0.00026919129 -0.00045342545 2830
|
||||
14800 1480 0.00026727674 -0.00047323419 2830
|
||||
15000 1500 0.0002663482 -0.00048423944 2830
|
||||
15200 1520 0.00026616663 -0.0004816085 2830
|
||||
15400 1540 0.00026634862 -0.00047573486 2830
|
||||
15600 1560 0.0002664314 -0.00046803192 2830
|
||||
15800 1580 0.00026603348 -0.00045753668 2830
|
||||
16000 1600 0.00026511015 -0.00044676105 2830
|
||||
16200 1620 0.00026373403 -0.00044075794 2830
|
||||
16400 1640 0.00026217342 -0.00043684036 2830
|
||||
16600 1660 0.0002607038 -0.00042774771 2830
|
||||
16800 1680 0.00025951097 -0.00041603026 2830
|
||||
17000 1700 0.00025869088 -0.00040302996 2830
|
||||
17200 1720 0.00025825588 -0.00038415247 2830
|
||||
17400 1740 0.00025818373 -0.00035742127 2830
|
||||
17600 1760 0.00025843381 -0.00032854722 2830
|
||||
17800 1780 0.00025897836 -0.00029821183 2830
|
||||
18000 1800 0.00025981472 -0.00026108907 2830
|
||||
18200 1820 0.00026095775 -0.00021731058 2830
|
||||
18400 1840 0.00026239688 -0.00017030825 2830
|
||||
18600 1860 0.00026404432 -0.00011868778 2830
|
||||
18800 1880 0.00026574247 -5.9556286e-05 2830
|
||||
19000 1900 0.00026729563 2.3014881e-06 2830
|
||||
19200 1920 0.00026852418 6.2100169e-05 2830
|
||||
19400 1940 0.00026929086 0.00012090325 2830
|
||||
19600 1960 0.0002695407 0.00017904223 2830
|
||||
19800 1980 0.00026929677 0.00023112254 2830
|
||||
20000 2000 0.00026863577 0.0002756697 2830
|
||||
20200 2020 0.00026765699 0.0003158399 2830
|
||||
20400 2040 0.00026646841 0.00035200747 2830
|
||||
20600 2060 0.00026516938 0.00038018442 2830
|
||||
20800 2080 0.00026383495 0.00040179111 2830
|
||||
21000 2100 0.00026252489 0.00042030921 2830
|
||||
21200 2120 0.00026128616 0.00043466976 2830
|
||||
21400 2140 0.00026014896 0.00044221445 2830
|
||||
21600 2160 0.00025912325 0.00044531883 2830
|
||||
21800 2180 0.00025821515 0.00044661709 2830
|
||||
22000 2200 0.00025742576 0.00044409089 2830
|
||||
22200 2220 0.00025674938 0.00043634999 2830
|
||||
22400 2240 0.00025617111 0.00042630344 2830
|
||||
22600 2260 0.0002556791 0.00041561603 2830
|
||||
22800 2280 0.00025525963 0.00040166735 2830
|
||||
23000 2300 0.00025489538 0.00038430419 2830
|
||||
23200 2320 0.00025456861 0.0003669402 2830
|
||||
23400 2340 0.00025426747 0.00034972373 2830
|
||||
23600 2360 0.00025398353 0.0003302242 2830
|
||||
23800 2380 0.00025370842 0.00030993088 2830
|
||||
24000 2400 0.00025344084 0.00029143258 2830
|
||||
24200 2420 0.00025318683 0.00027421708 2830
|
||||
24400 2440 0.0002529591 0.00025603123 2830
|
||||
24600 2460 0.0002527713 0.00023950245 2830
|
||||
24800 2480 0.00025264228 0.00022644812 2830
|
||||
25000 2500 0.00025259021 0.00021540748 2830
|
||||
25200 2520 0.00025262892 0.00020544201 2830
|
||||
25400 2540 0.00025276229 0.00019845807 2830
|
||||
25600 2560 0.0002529876 0.00019449958 2830
|
||||
25800 2580 0.00025329374 0.00019082606 2830
|
||||
26000 2600 0.00025366066 0.00018700064 2830
|
||||
26200 2620 0.00025406164 0.00018426061 2830
|
||||
26400 2640 0.00025446737 0.00018098339 2830
|
||||
26600 2660 0.00025484714 0.00017471869 2830
|
||||
26800 2680 0.00025516604 0.00016565557 2830
|
||||
27000 2700 0.00025538911 0.00015493626 2830
|
||||
27200 2720 0.00025548177 0.00014075592 2830
|
||||
27400 2740 0.00025541168 0.00012205573 2830
|
||||
27600 2760 0.00025514889 0.00010039772 2830
|
||||
27800 2780 0.00025467547 7.7069215e-05 2830
|
||||
28000 2800 0.0002539915 5.1158042e-05 2830
|
||||
28200 2820 0.00025312083 2.3468384e-05 2830
|
||||
28400 2840 0.00025211323 -3.2184465e-06 2830
|
||||
28600 2860 0.00025104366 -2.7726301e-05 2830
|
||||
28800 2880 0.00025000263 -5.0202987e-05 2830
|
||||
29000 2900 0.00024907814 -6.9244776e-05 2830
|
||||
29200 2920 0.00024833815 -8.2874516e-05 2830
|
||||
29400 2940 0.0002478155 -9.1854992e-05 2830
|
||||
29600 2960 0.00024750313 -9.766055e-05 2830
|
||||
29800 2980 0.00024735538 -9.9681291e-05 2830
|
||||
30000 3000 0.00024730191 -9.818759e-05 2830
|
||||
Loop time of 177.982 on 4 procs for 30000 steps with 2830 atoms
|
||||
|
||||
Performance: 1456330.235 tau/day, 168.557 timesteps/s, 477.016 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 22.913 | 27.061 | 34.594 | 87.2 | 15.20
|
||||
Bond | 0.22386 | 0.26159 | 0.30792 | 6.0 | 0.15
|
||||
Neigh | 0.84412 | 0.84509 | 0.8462 | 0.1 | 0.47
|
||||
Comm | 0.50015 | 0.55579 | 0.60346 | 5.2 | 0.31
|
||||
Output | 0.65854 | 0.69412 | 0.72473 | 2.8 | 0.39
|
||||
Modify | 133.13 | 136 | 137.38 | 14.5 | 76.41
|
||||
Other | | 12.57 | | | 7.06
|
||||
|
||||
Nlocal: 707.5 ave 1576 max 53 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 164.75 ave 239 max 94 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 12307.8 ave 27380 max 983 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
FullNghs: 23517 ave 53040 max 1502 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 94068
|
||||
Ave neighs/atom = 33.239576
|
||||
Ave special neighs/atom = 0.89257951
|
||||
Neighbor list builds = 783
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:58
|
||||
76
examples/rheo/dam-break/in.rheo.dam.break
Normal file
76
examples/rheo/dam-break/in.rheo.dam.break
Normal file
@ -0,0 +1,76 @@
|
||||
# ------ 2D dam break ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary f s p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 2.2
|
||||
variable dx equal 3.0
|
||||
|
||||
region box block -1 150 -1 80 -0.1 0.1 units box
|
||||
create_box 2 box
|
||||
lattice hex ${n}
|
||||
|
||||
region fluid block $(xlo+v_dx+1.0) $(xlo+40.0) $(ylo+v_dx+1.0) $(yhi-20.0) EDGE EDGE units box
|
||||
region walls1 block $(xlo+v_dx) $(xhi-v_dx) $(ylo+v_dx) $(yhi-v_dx) EDGE EDGE side out units box
|
||||
region walls2 block EDGE EDGE EDGE $(yhi-v_dx) EDGE EDGE side in units box
|
||||
region walls intersect 2 walls1 walls2
|
||||
|
||||
create_atoms 1 region fluid
|
||||
create_atoms 2 region walls
|
||||
|
||||
group fluid type 1
|
||||
group rig type 2
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable cs equal 1.0
|
||||
variable zeta equal 0.1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.1
|
||||
variable Dr equal 0.1
|
||||
|
||||
mass 1 ${mp}
|
||||
mass 2 $(2*v_mp)
|
||||
set group all rheo/rho ${rho0}
|
||||
|
||||
set group all rheo/status 0
|
||||
set group rig rheo/status 1
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} #rho/damp ${Dr}
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 10 &
|
||||
surface/detection coordination 22 8 &
|
||||
rho/sum
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all gravity 1e-3 vector 0 -1 0
|
||||
fix 5 rig setforce 0.0 0.0 0.0
|
||||
fix 6 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute p all rheo/property/atom pressure
|
||||
compute surf all rheo/property/atom surface
|
||||
compute sn all rheo/property/atom surface/n/x surface/n/y
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time ke press
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho c_surf c_p c_sn[*]
|
||||
|
||||
run 30000
|
||||
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
82
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
82
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
@ -0,0 +1,82 @@
|
||||
# ------ 2D Ice Cube Pour ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
region box block -25 25 0 100 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
|
||||
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
lattice sq 1.0
|
||||
create_atoms 1 region fluid
|
||||
|
||||
set group all sph/e 8.0
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# ------ Pour particles ------#
|
||||
|
||||
molecule my_mol "square.mol"
|
||||
|
||||
# Wall region extends far enough in z to avoid contact
|
||||
region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
|
||||
region drop block -16 16 70 90 EDGE EDGE side in units box
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
thermal &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} &
|
||||
specific/heat * constant ${Cv} &
|
||||
Tfreeze * constant ${Tf} &
|
||||
latent/heat * constant ${L} &
|
||||
react 1.5 1
|
||||
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
|
||||
fix 6 all gravity 5e-4 vector 0 -1 0
|
||||
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
|
||||
fix 8 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||
|
||||
run 30000
|
||||
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
@ -0,0 +1,379 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D Ice Cube Pour ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
region box block -25 25 0 100 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
Created orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 1 $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 1 30 EDGE EDGE units box
|
||||
lattice sq 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
create_atoms 1 region fluid
|
||||
Created 1470 atoms
|
||||
using lattice units in orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
set group all sph/e 8.0
|
||||
Setting atom values ...
|
||||
1470 settings made for sph/e
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable kappa equal 0.01*1/${mp}
|
||||
variable kappa equal 0.01*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# ------ Pour particles ------#
|
||||
|
||||
molecule my_mol "square.mol"
|
||||
Read molecule template my_mol:
|
||||
#Made with create_mol.py
|
||||
1 molecules
|
||||
0 fragments
|
||||
100 atoms with max type 1
|
||||
342 bonds with max type 1
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
|
||||
# Wall region extends far enough in z to avoid contact
|
||||
region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
|
||||
region drop block -16 16 70 90 EDGE EDGE side in units box
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 1 react 1.5 1
|
||||
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
|
||||
fix 6 all gravity 5e-4 vector 0 -1 0
|
||||
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
|
||||
WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1881)
|
||||
fix 8 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||
|
||||
run 30000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
- @article{ApplMathModel.130.310,
|
||||
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||
journal = {Applied Mathematical Modelling},
|
||||
volume = {130},
|
||||
pages = {310-326},
|
||||
year = {2024},
|
||||
issn = {0307-904X},
|
||||
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 31 61 1
|
||||
7 neighbor lists, perpetual/occasional/extra = 6 1 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (4)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) fix rheo/thermal, occasional, trim from (4)
|
||||
attributes: half, newton off, cut 3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.53 | 15.61 | 15.69 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0 0 1470
|
||||
200 20 5.6002982e-05 3.4434234e-05 1570
|
||||
400 40 8.2173099e-05 8.6171768e-05 1570
|
||||
600 60 8.019018e-05 0.00010750355 1570
|
||||
800 80 0.00013866953 0.00010265608 1570
|
||||
1000 100 0.00018965028 8.1985605e-05 1570
|
||||
1200 120 0.00022033242 7.4736443e-05 1670
|
||||
1400 140 0.00030767062 0.00011264333 1670
|
||||
1600 160 0.00040770127 0.00018779992 1670
|
||||
1800 180 0.00047476332 0.00023153009 1670
|
||||
2000 200 0.00059116774 0.00027200445 1670
|
||||
2200 220 0.0007151733 0.0002919963 1770
|
||||
2400 240 0.00083392135 0.00029757889 1770
|
||||
2600 260 0.00099653466 0.00036547269 1770
|
||||
2800 280 0.0011964069 0.00045983458 1770
|
||||
3000 300 0.0013716953 0.00055013647 1770
|
||||
3200 320 0.0015174096 0.00064203572 1870
|
||||
3400 340 0.0016539743 0.00086671622 1870
|
||||
3600 360 0.0015887858 0.00066353749 1870
|
||||
3800 380 0.0016451684 0.00070551483 1870
|
||||
4000 400 0.0017330971 0.00080722283 1870
|
||||
4200 420 0.001812193 0.00073573903 1970
|
||||
4400 440 0.001755871 0.0010621909 1970
|
||||
4600 460 0.0016190772 0.00072913706 1970
|
||||
4800 480 0.0015741931 0.00073524088 1970
|
||||
5000 500 0.0016488815 0.00088684275 1970
|
||||
5200 520 0.0017213288 0.00077042378 2070
|
||||
5400 540 0.0018509598 0.0010219434 2070
|
||||
5600 560 0.0020251064 0.00083182483 2070
|
||||
5800 580 0.0022473255 0.00095076144 2070
|
||||
6000 600 0.0024843519 0.0011247014 2070
|
||||
6200 620 0.0022282321 0.0018105932 2170
|
||||
6400 640 0.0020289063 0.0014158497 2170
|
||||
6600 660 0.002145241 0.0011359383 2170
|
||||
6800 680 0.0024313937 0.0016475504 2170
|
||||
7000 700 0.0021000599 0.0020983745 2170
|
||||
7200 720 0.0019137235 0.0010439152 2270
|
||||
7400 740 0.0018801367 0.00095436448 2270
|
||||
7600 760 0.0017979449 0.0011184039 2270
|
||||
7800 780 0.0018005205 0.0009243205 2270
|
||||
8000 800 0.0017827073 0.0013671228 2270
|
||||
8200 820 0.0018387108 0.0015426012 2270
|
||||
8400 840 0.0016000788 0.0016751514 2270
|
||||
8600 860 0.0013954964 0.0016884335 2270
|
||||
8800 880 0.0013283728 0.0012399398 2270
|
||||
9000 900 0.001389385 0.0012968496 2270
|
||||
9200 920 0.0012295438 0.0012995821 2270
|
||||
9400 940 0.0010522655 0.00082245528 2270
|
||||
9600 960 0.00097085496 0.00053833131 2270
|
||||
9800 980 0.0009398987 0.00063467387 2270
|
||||
10000 1000 0.00092710392 0.00059494446 2270
|
||||
10200 1020 0.00095545471 0.00074560644 2270
|
||||
10400 1040 0.0009645841 0.00085429807 2270
|
||||
10600 1060 0.00064037148 0.0017222246 2270
|
||||
10800 1080 0.00046790978 0.00088204234 2270
|
||||
11000 1100 0.00030106229 0.00074950209 2270
|
||||
11200 1120 0.00027746016 0.00052831745 2270
|
||||
11400 1140 0.0002533348 0.0006272715 2270
|
||||
11600 1160 0.00021825085 0.00029691552 2270
|
||||
11800 1180 0.0001451308 0.00015037478 2270
|
||||
12000 1200 0.0001314823 0.00017227174 2270
|
||||
12200 1220 0.00013693632 0.00017791384 2270
|
||||
12400 1240 0.00014987347 0.0002286677 2270
|
||||
12600 1260 0.00015092598 0.0003698436 2270
|
||||
12800 1280 0.0001291653 0.00047229532 2270
|
||||
13000 1300 0.00011949988 0.00049560375 2270
|
||||
13200 1320 0.00011694665 0.00057542084 2270
|
||||
13400 1340 9.6164519e-05 0.00062714755 2270
|
||||
13600 1360 8.4517591e-05 0.00044156913 2270
|
||||
13800 1380 0.00019140516 0.0003264745 2270
|
||||
14000 1400 0.00013868599 0.00037753497 2270
|
||||
14200 1420 9.3701636e-05 0.00031517848 2270
|
||||
14400 1440 6.7389077e-05 0.0002946861 2270
|
||||
14600 1460 5.3640086e-05 0.00026650711 2270
|
||||
14800 1480 4.2699992e-05 0.00023789279 2270
|
||||
15000 1500 5.3012016e-05 0.00019933234 2270
|
||||
15200 1520 5.8834197e-05 0.00022407007 2270
|
||||
15400 1540 5.0899982e-05 0.00029695531 2270
|
||||
15600 1560 3.0476742e-05 0.00039119066 2270
|
||||
15800 1580 1.6633264e-05 0.00033770401 2270
|
||||
16000 1600 1.098906e-05 0.00036684894 2270
|
||||
16200 1620 1.464848e-05 0.00036449759 2270
|
||||
16400 1640 1.9598429e-05 0.00021056689 2270
|
||||
16600 1660 1.2644955e-05 0.00020781781 2270
|
||||
16800 1680 8.8428553e-06 0.000165 2270
|
||||
17000 1700 8.8971439e-06 0.00012266475 2270
|
||||
17200 1720 1.7032781e-05 0.00019873443 2270
|
||||
17400 1740 1.9448563e-05 0.00025661663 2270
|
||||
17600 1760 1.3714713e-05 0.000324022 2270
|
||||
17800 1780 9.1326468e-06 0.00031392513 2270
|
||||
18000 1800 9.2464802e-06 0.00029729527 2270
|
||||
18200 1820 1.5553042e-05 0.00027488475 2270
|
||||
18400 1840 1.4132933e-05 0.00019565459 2270
|
||||
18600 1860 9.4734832e-06 0.00016716988 2270
|
||||
18800 1880 5.5115145e-06 0.00013728033 2270
|
||||
19000 1900 8.268812e-06 0.00015119605 2270
|
||||
19200 1920 1.2470136e-05 0.00020222131 2270
|
||||
19400 1940 9.9387775e-06 0.00024503373 2270
|
||||
19600 1960 5.4241999e-06 0.00026921858 2270
|
||||
19800 1980 2.7987348e-06 0.00026201267 2270
|
||||
20000 2000 6.272538e-06 0.00025626323 2270
|
||||
20200 2020 8.0157781e-06 0.000220139 2270
|
||||
20400 2040 6.1652093e-06 0.00017089058 2270
|
||||
20600 2060 2.9967592e-06 0.00014582864 2270
|
||||
20800 2080 3.016678e-06 0.000148629 2270
|
||||
21000 2100 7.287645e-06 0.00016486102 2270
|
||||
21200 2120 8.6905277e-06 0.00020276916 2270
|
||||
21400 2140 6.8453018e-06 0.00023156153 2270
|
||||
21600 2160 3.3853799e-06 0.0002432462 2270
|
||||
21800 2180 4.1241209e-06 0.00022829024 2270
|
||||
22000 2200 7.0802396e-06 0.00020784823 2270
|
||||
22200 2220 7.3361691e-06 0.00018114134 2270
|
||||
22400 2240 5.0764593e-06 0.00014351106 2270
|
||||
22600 2260 2.7487537e-06 0.00012919872 2270
|
||||
22800 2280 4.620167e-06 0.00013746218 2270
|
||||
23000 2300 6.9819357e-06 0.00015985102 2270
|
||||
23200 2320 6.8923916e-06 0.00018713045 2270
|
||||
23400 2340 4.1795088e-06 0.00019846682 2270
|
||||
23600 2360 2.2871028e-06 0.00021068421 2270
|
||||
23800 2380 3.862046e-06 0.00019553306 2270
|
||||
24000 2400 5.2448555e-06 0.00017398041 2270
|
||||
24200 2420 4.7565441e-06 0.00015008142 2270
|
||||
24400 2440 2.2952135e-06 0.00012747106 2270
|
||||
24600 2460 2.1575617e-06 0.00012516996 2270
|
||||
24800 2480 4.1777868e-06 0.0001331902 2270
|
||||
25000 2500 5.5679133e-06 0.00015504562 2270
|
||||
25200 2520 4.5758741e-06 0.00017146032 2270
|
||||
25400 2540 2.3403277e-06 0.00017611666 2270
|
||||
25600 2560 2.7029302e-06 0.00016850788 2270
|
||||
25800 2580 4.3601102e-06 0.00015884642 2270
|
||||
26000 2600 5.2244249e-06 0.00013793898 2270
|
||||
26200 2620 3.4577672e-06 0.00012395875 2270
|
||||
26400 2640 2.361577e-06 0.00011600057 2270
|
||||
26600 2660 2.8515644e-06 0.00011277063 2270
|
||||
26800 2680 4.0851213e-06 0.0001290832 2270
|
||||
27000 2700 4.2579644e-06 0.0001476495 2270
|
||||
27200 2720 2.6593858e-06 0.00015977745 2270
|
||||
27400 2740 1.990115e-06 0.00015612787 2270
|
||||
27600 2760 2.6756835e-06 0.00014913772 2270
|
||||
27800 2780 3.9032806e-06 0.00014014763 2270
|
||||
28000 2800 3.2729446e-06 0.00012216846 2270
|
||||
28200 2820 1.9357278e-06 0.00011078621 2270
|
||||
28400 2840 1.7094832e-06 0.00010910509 2270
|
||||
28600 2860 2.8731406e-06 0.00011179644 2270
|
||||
28800 2880 3.7062354e-06 0.00012254091 2270
|
||||
29000 2900 2.7844262e-06 0.00013060331 2270
|
||||
29200 2920 1.7680655e-06 0.00013797514 2270
|
||||
29400 2940 1.706873e-06 0.0001350685 2270
|
||||
29600 2960 2.8764562e-06 0.00012428508 2270
|
||||
29800 2980 3.1502029e-06 0.00011456718 2270
|
||||
30000 3000 2.1833409e-06 0.00010317469 2270
|
||||
Loop time of 165.611 on 4 procs for 30000 steps with 2270 atoms
|
||||
|
||||
Performance: 1565111.240 tau/day, 181.147 timesteps/s, 411.204 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.63183 | 21.226 | 42.266 | 444.6 | 12.82
|
||||
Bond | 0.095073 | 0.17799 | 0.27877 | 17.0 | 0.11
|
||||
Neigh | 2.0745 | 2.0781 | 2.0822 | 0.2 | 1.25
|
||||
Comm | 0.32024 | 0.38703 | 0.45564 | 8.1 | 0.23
|
||||
Output | 0.60459 | 0.76798 | 0.93724 | 18.6 | 0.46
|
||||
Modify | 119.85 | 140.76 | 161.36 | 172.2 | 85.00
|
||||
Other | | 0.2124 | | | 0.13
|
||||
|
||||
Nlocal: 567.5 ave 1139 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 75.5 ave 152 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 9238.25 ave 18490 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 17945 ave 35917 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 71780
|
||||
Ave neighs/atom = 31.621145
|
||||
Ave special neighs/atom = 0.22026432
|
||||
Neighbor list builds = 2071
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:02:45
|
||||
658
examples/rheo/ice-cubes/square.mol
Normal file
658
examples/rheo/ice-cubes/square.mol
Normal file
@ -0,0 +1,658 @@
|
||||
#Made with create_mol.py
|
||||
|
||||
100 atoms
|
||||
342 bonds
|
||||
|
||||
Coords
|
||||
#ID x y z
|
||||
1 -4 -4 0
|
||||
2 -3 -4 0
|
||||
3 -2 -4 0
|
||||
4 -1 -4 0
|
||||
5 0 -4 0
|
||||
6 1 -4 0
|
||||
7 2 -4 0
|
||||
8 3 -4 0
|
||||
9 4 -4 0
|
||||
10 5 -4 0
|
||||
11 -4 -3 0
|
||||
12 -3 -3 0
|
||||
13 -2 -3 0
|
||||
14 -1 -3 0
|
||||
15 0 -3 0
|
||||
16 1 -3 0
|
||||
17 2 -3 0
|
||||
18 3 -3 0
|
||||
19 4 -3 0
|
||||
20 5 -3 0
|
||||
21 -4 -2 0
|
||||
22 -3 -2 0
|
||||
23 -2 -2 0
|
||||
24 -1 -2 0
|
||||
25 0 -2 0
|
||||
26 1 -2 0
|
||||
27 2 -2 0
|
||||
28 3 -2 0
|
||||
29 4 -2 0
|
||||
30 5 -2 0
|
||||
31 -4 -1 0
|
||||
32 -3 -1 0
|
||||
33 -2 -1 0
|
||||
34 -1 -1 0
|
||||
35 0 -1 0
|
||||
36 1 -1 0
|
||||
37 2 -1 0
|
||||
38 3 -1 0
|
||||
39 4 -1 0
|
||||
40 5 -1 0
|
||||
41 -4 0 0
|
||||
42 -3 0 0
|
||||
43 -2 0 0
|
||||
44 -1 0 0
|
||||
45 0 0 0
|
||||
46 1 0 0
|
||||
47 2 0 0
|
||||
48 3 0 0
|
||||
49 4 0 0
|
||||
50 5 0 0
|
||||
51 -4 1 0
|
||||
52 -3 1 0
|
||||
53 -2 1 0
|
||||
54 -1 1 0
|
||||
55 0 1 0
|
||||
56 1 1 0
|
||||
57 2 1 0
|
||||
58 3 1 0
|
||||
59 4 1 0
|
||||
60 5 1 0
|
||||
61 -4 2 0
|
||||
62 -3 2 0
|
||||
63 -2 2 0
|
||||
64 -1 2 0
|
||||
65 0 2 0
|
||||
66 1 2 0
|
||||
67 2 2 0
|
||||
68 3 2 0
|
||||
69 4 2 0
|
||||
70 5 2 0
|
||||
71 -4 3 0
|
||||
72 -3 3 0
|
||||
73 -2 3 0
|
||||
74 -1 3 0
|
||||
75 0 3 0
|
||||
76 1 3 0
|
||||
77 2 3 0
|
||||
78 3 3 0
|
||||
79 4 3 0
|
||||
80 5 3 0
|
||||
81 -4 4 0
|
||||
82 -3 4 0
|
||||
83 -2 4 0
|
||||
84 -1 4 0
|
||||
85 0 4 0
|
||||
86 1 4 0
|
||||
87 2 4 0
|
||||
88 3 4 0
|
||||
89 4 4 0
|
||||
90 5 4 0
|
||||
91 -4 5 0
|
||||
92 -3 5 0
|
||||
93 -2 5 0
|
||||
94 -1 5 0
|
||||
95 0 5 0
|
||||
96 1 5 0
|
||||
97 2 5 0
|
||||
98 3 5 0
|
||||
99 4 5 0
|
||||
100 5 5 0
|
||||
|
||||
Types
|
||||
#ID type
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Masses
|
||||
#ID mass
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Bonds
|
||||
#ID type atom1 atom2
|
||||
1 1 1 2
|
||||
2 1 1 11
|
||||
3 1 1 12
|
||||
4 1 2 3
|
||||
5 1 2 11
|
||||
6 1 2 12
|
||||
7 1 2 13
|
||||
8 1 3 4
|
||||
9 1 3 12
|
||||
10 1 3 13
|
||||
11 1 3 14
|
||||
12 1 4 5
|
||||
13 1 4 13
|
||||
14 1 4 14
|
||||
15 1 4 15
|
||||
16 1 5 6
|
||||
17 1 5 14
|
||||
18 1 5 15
|
||||
19 1 5 16
|
||||
20 1 6 7
|
||||
21 1 6 15
|
||||
22 1 6 16
|
||||
23 1 6 17
|
||||
24 1 7 8
|
||||
25 1 7 16
|
||||
26 1 7 17
|
||||
27 1 7 18
|
||||
28 1 8 9
|
||||
29 1 8 17
|
||||
30 1 8 18
|
||||
31 1 8 19
|
||||
32 1 9 10
|
||||
33 1 9 18
|
||||
34 1 9 19
|
||||
35 1 9 20
|
||||
36 1 10 19
|
||||
37 1 10 20
|
||||
38 1 11 21
|
||||
39 1 11 12
|
||||
40 1 11 22
|
||||
41 1 12 21
|
||||
42 1 12 13
|
||||
43 1 12 22
|
||||
44 1 12 23
|
||||
45 1 13 22
|
||||
46 1 13 23
|
||||
47 1 13 14
|
||||
48 1 13 24
|
||||
49 1 14 23
|
||||
50 1 14 24
|
||||
51 1 14 15
|
||||
52 1 14 25
|
||||
53 1 15 24
|
||||
54 1 15 16
|
||||
55 1 15 25
|
||||
56 1 15 26
|
||||
57 1 16 25
|
||||
58 1 16 26
|
||||
59 1 16 17
|
||||
60 1 16 27
|
||||
61 1 17 26
|
||||
62 1 17 18
|
||||
63 1 17 27
|
||||
64 1 17 28
|
||||
65 1 18 27
|
||||
66 1 18 28
|
||||
67 1 18 19
|
||||
68 1 18 29
|
||||
69 1 19 28
|
||||
70 1 19 29
|
||||
71 1 19 20
|
||||
72 1 19 30
|
||||
73 1 20 29
|
||||
74 1 20 30
|
||||
75 1 21 22
|
||||
76 1 21 31
|
||||
77 1 21 32
|
||||
78 1 22 23
|
||||
79 1 22 31
|
||||
80 1 22 32
|
||||
81 1 22 33
|
||||
82 1 23 24
|
||||
83 1 23 32
|
||||
84 1 23 33
|
||||
85 1 23 34
|
||||
86 1 24 25
|
||||
87 1 24 33
|
||||
88 1 24 34
|
||||
89 1 24 35
|
||||
90 1 25 26
|
||||
91 1 25 34
|
||||
92 1 25 35
|
||||
93 1 25 36
|
||||
94 1 26 27
|
||||
95 1 26 35
|
||||
96 1 26 36
|
||||
97 1 26 37
|
||||
98 1 27 28
|
||||
99 1 27 36
|
||||
100 1 27 37
|
||||
101 1 27 38
|
||||
102 1 28 29
|
||||
103 1 28 37
|
||||
104 1 28 38
|
||||
105 1 28 39
|
||||
106 1 29 30
|
||||
107 1 29 38
|
||||
108 1 29 39
|
||||
109 1 29 40
|
||||
110 1 30 39
|
||||
111 1 30 40
|
||||
112 1 31 32
|
||||
113 1 31 41
|
||||
114 1 31 42
|
||||
115 1 32 33
|
||||
116 1 32 41
|
||||
117 1 32 42
|
||||
118 1 32 43
|
||||
119 1 33 34
|
||||
120 1 33 42
|
||||
121 1 33 43
|
||||
122 1 33 44
|
||||
123 1 34 35
|
||||
124 1 34 43
|
||||
125 1 34 44
|
||||
126 1 34 45
|
||||
127 1 35 36
|
||||
128 1 35 44
|
||||
129 1 35 45
|
||||
130 1 35 46
|
||||
131 1 36 37
|
||||
132 1 36 45
|
||||
133 1 36 46
|
||||
134 1 36 47
|
||||
135 1 37 38
|
||||
136 1 37 46
|
||||
137 1 37 47
|
||||
138 1 37 48
|
||||
139 1 38 39
|
||||
140 1 38 47
|
||||
141 1 38 48
|
||||
142 1 38 49
|
||||
143 1 39 40
|
||||
144 1 39 48
|
||||
145 1 39 49
|
||||
146 1 39 50
|
||||
147 1 40 49
|
||||
148 1 40 50
|
||||
149 1 41 51
|
||||
150 1 41 42
|
||||
151 1 41 52
|
||||
152 1 42 51
|
||||
153 1 42 43
|
||||
154 1 42 52
|
||||
155 1 42 53
|
||||
156 1 43 52
|
||||
157 1 43 53
|
||||
158 1 43 44
|
||||
159 1 43 54
|
||||
160 1 44 53
|
||||
161 1 44 54
|
||||
162 1 44 45
|
||||
163 1 44 55
|
||||
164 1 45 54
|
||||
165 1 45 46
|
||||
166 1 45 55
|
||||
167 1 45 56
|
||||
168 1 46 55
|
||||
169 1 46 56
|
||||
170 1 46 47
|
||||
171 1 46 57
|
||||
172 1 47 56
|
||||
173 1 47 48
|
||||
174 1 47 57
|
||||
175 1 47 58
|
||||
176 1 48 57
|
||||
177 1 48 58
|
||||
178 1 48 49
|
||||
179 1 48 59
|
||||
180 1 49 58
|
||||
181 1 49 59
|
||||
182 1 49 50
|
||||
183 1 49 60
|
||||
184 1 50 59
|
||||
185 1 50 60
|
||||
186 1 51 52
|
||||
187 1 51 61
|
||||
188 1 51 62
|
||||
189 1 52 53
|
||||
190 1 52 61
|
||||
191 1 52 62
|
||||
192 1 52 63
|
||||
193 1 53 54
|
||||
194 1 53 62
|
||||
195 1 53 63
|
||||
196 1 53 64
|
||||
197 1 54 55
|
||||
198 1 54 63
|
||||
199 1 54 64
|
||||
200 1 54 65
|
||||
201 1 55 56
|
||||
202 1 55 64
|
||||
203 1 55 65
|
||||
204 1 55 66
|
||||
205 1 56 57
|
||||
206 1 56 65
|
||||
207 1 56 66
|
||||
208 1 56 67
|
||||
209 1 57 58
|
||||
210 1 57 66
|
||||
211 1 57 67
|
||||
212 1 57 68
|
||||
213 1 58 59
|
||||
214 1 58 67
|
||||
215 1 58 68
|
||||
216 1 58 69
|
||||
217 1 59 60
|
||||
218 1 59 68
|
||||
219 1 59 69
|
||||
220 1 59 70
|
||||
221 1 60 69
|
||||
222 1 60 70
|
||||
223 1 61 71
|
||||
224 1 61 62
|
||||
225 1 61 72
|
||||
226 1 62 71
|
||||
227 1 62 63
|
||||
228 1 62 72
|
||||
229 1 62 73
|
||||
230 1 63 72
|
||||
231 1 63 73
|
||||
232 1 63 64
|
||||
233 1 63 74
|
||||
234 1 64 73
|
||||
235 1 64 74
|
||||
236 1 64 65
|
||||
237 1 64 75
|
||||
238 1 65 74
|
||||
239 1 65 66
|
||||
240 1 65 75
|
||||
241 1 65 76
|
||||
242 1 66 75
|
||||
243 1 66 76
|
||||
244 1 66 67
|
||||
245 1 66 77
|
||||
246 1 67 76
|
||||
247 1 67 68
|
||||
248 1 67 77
|
||||
249 1 67 78
|
||||
250 1 68 77
|
||||
251 1 68 78
|
||||
252 1 68 69
|
||||
253 1 68 79
|
||||
254 1 69 78
|
||||
255 1 69 79
|
||||
256 1 69 70
|
||||
257 1 69 80
|
||||
258 1 70 79
|
||||
259 1 70 80
|
||||
260 1 71 72
|
||||
261 1 71 81
|
||||
262 1 71 82
|
||||
263 1 72 73
|
||||
264 1 72 81
|
||||
265 1 72 82
|
||||
266 1 72 83
|
||||
267 1 73 74
|
||||
268 1 73 82
|
||||
269 1 73 83
|
||||
270 1 73 84
|
||||
271 1 74 75
|
||||
272 1 74 83
|
||||
273 1 74 84
|
||||
274 1 74 85
|
||||
275 1 75 76
|
||||
276 1 75 84
|
||||
277 1 75 85
|
||||
278 1 75 86
|
||||
279 1 76 77
|
||||
280 1 76 85
|
||||
281 1 76 86
|
||||
282 1 76 87
|
||||
283 1 77 78
|
||||
284 1 77 86
|
||||
285 1 77 87
|
||||
286 1 77 88
|
||||
287 1 78 79
|
||||
288 1 78 87
|
||||
289 1 78 88
|
||||
290 1 78 89
|
||||
291 1 79 80
|
||||
292 1 79 88
|
||||
293 1 79 89
|
||||
294 1 79 90
|
||||
295 1 80 89
|
||||
296 1 80 90
|
||||
297 1 81 82
|
||||
298 1 81 91
|
||||
299 1 81 92
|
||||
300 1 82 83
|
||||
301 1 82 91
|
||||
302 1 82 92
|
||||
303 1 82 93
|
||||
304 1 83 84
|
||||
305 1 83 92
|
||||
306 1 83 93
|
||||
307 1 83 94
|
||||
308 1 84 85
|
||||
309 1 84 93
|
||||
310 1 84 94
|
||||
311 1 84 95
|
||||
312 1 85 86
|
||||
313 1 85 94
|
||||
314 1 85 95
|
||||
315 1 85 96
|
||||
316 1 86 87
|
||||
317 1 86 95
|
||||
318 1 86 96
|
||||
319 1 86 97
|
||||
320 1 87 88
|
||||
321 1 87 96
|
||||
322 1 87 97
|
||||
323 1 87 98
|
||||
324 1 88 89
|
||||
325 1 88 97
|
||||
326 1 88 98
|
||||
327 1 88 99
|
||||
328 1 89 90
|
||||
329 1 89 98
|
||||
330 1 89 99
|
||||
331 1 89 100
|
||||
332 1 90 99
|
||||
333 1 90 100
|
||||
334 1 91 92
|
||||
335 1 92 93
|
||||
336 1 93 94
|
||||
337 1 94 95
|
||||
338 1 95 96
|
||||
339 1 96 97
|
||||
340 1 97 98
|
||||
341 1 98 99
|
||||
342 1 99 100
|
||||
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
@ -0,0 +1,102 @@
|
||||
# ------ 2D oxidizing bar ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -60 60 0 80 -0.01 0.01 units box
|
||||
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
|
||||
region lbar block -15 0 3 80 EDGE EDGE units box
|
||||
region rbar block 0 15 3 80 EDGE EDGE units box
|
||||
region bar union 2 lbar rbar
|
||||
region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
|
||||
|
||||
lattice hex 1.0
|
||||
create_atoms 1 region bar
|
||||
create_atoms 3 region floor
|
||||
|
||||
set region rbar type 2
|
||||
group bar type 1 2
|
||||
group rbar type 2
|
||||
group floor type 3
|
||||
|
||||
set group all sph/e 0.0
|
||||
set group all rheo/status 1
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.1*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 0.1
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
create_bonds many bar bar 1 0 1.5
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style hybrid bpm/spring rheo/shell t/form 100
|
||||
bond_coeff 1 bpm/spring 1.0 1.0 1.0
|
||||
bond_coeff 2 rheo/shell 0.2 0.2 0.1
|
||||
|
||||
# ------ Apply dynamics ------#
|
||||
|
||||
# Note: surface detection is not performed on solid bodies, so cannot use surface property
|
||||
compute coord all rheo/property/atom coordination
|
||||
variable surf atom c_coord<22
|
||||
group surf dynamic all var surf every 10
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
thermal &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} &
|
||||
specific/heat * constant ${Cv} &
|
||||
Tfreeze * constant ${Tf} &
|
||||
latent/heat * constant ${L} &
|
||||
react 1.5 1
|
||||
|
||||
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||
fix 8 floor setforce 0.0 0.0 0.0
|
||||
fix 9 surf add/heat linear 1.1 0.05
|
||||
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||
fix 11 all enforce2d
|
||||
|
||||
compute surf all rheo/property/atom surface
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond_shell all rheo/property/atom nbond/shell
|
||||
compute nbond_solid all nbond/atom bond/type 1
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf
|
||||
|
||||
run 40000
|
||||
488
examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4
Normal file
488
examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4
Normal file
@ -0,0 +1,488 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D oxidizing bar ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -60 60 0 80 -0.01 0.01 units box
|
||||
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region lbar block -15 0 3 80 EDGE EDGE units box
|
||||
region rbar block 0 15 3 80 EDGE EDGE units box
|
||||
region bar union 2 lbar rbar
|
||||
region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
|
||||
|
||||
lattice hex 1.0
|
||||
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||
create_atoms 1 region bar
|
||||
Created 2255 atoms
|
||||
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 3 region floor
|
||||
Created 446 atoms
|
||||
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set region rbar type 2
|
||||
Setting atom values ...
|
||||
1148 settings made for type
|
||||
group bar type 1 2
|
||||
2255 atoms in group bar
|
||||
group rbar type 2
|
||||
1148 atoms in group rbar
|
||||
group floor type 3
|
||||
446 atoms in group floor
|
||||
|
||||
set group all sph/e 0.0
|
||||
Setting atom values ...
|
||||
2701 settings made for sph/e
|
||||
set group all rheo/status 1
|
||||
Setting atom values ...
|
||||
2701 settings made for rheo/status
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.1*${rho0}/${mp}
|
||||
variable kappa equal 0.1*1/${mp}
|
||||
variable kappa equal 0.1*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 0.1
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
create_bonds many bar bar 1 0 1.5
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 73 49 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair rheo, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) pair rheo/solid, perpetual, trim from (2)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Added 6547 bonds, new total = 6547
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
6 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style hybrid bpm/spring rheo/shell t/form 100
|
||||
bond_coeff 1 bpm/spring 1.0 1.0 1.0
|
||||
bond_coeff 2 rheo/shell 0.2 0.2 0.1
|
||||
|
||||
# ------ Apply dynamics ------#
|
||||
|
||||
# Note: surface detection is not performed on solid bodies, so cannot use surface property
|
||||
compute coord all rheo/property/atom coordination
|
||||
variable surf atom c_coord<22
|
||||
group surf dynamic all var surf every 10
|
||||
dynamic group surf defined
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 0.1 react 1.5 1
|
||||
|
||||
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||
fix 8 floor setforce 0.0 0.0 0.0
|
||||
fix 9 surf add/heat linear 1.1 0.05
|
||||
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||
fix 11 all enforce2d
|
||||
|
||||
compute surf all rheo/property/atom surface
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute status all rheo/property/atom status
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond_shell all rheo/property/atom nbond/shell
|
||||
compute nbond_solid all nbond/atom bond/type 1
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status
|
||||
|
||||
run 40000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
- @article{ApplMathModel.130.310,
|
||||
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||
journal = {Applied Mathematical Modelling},
|
||||
volume = {130},
|
||||
pages = {310-326},
|
||||
year = {2024},
|
||||
issn = {0307-904X},
|
||||
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 73 49 1
|
||||
8 neighbor lists, perpetual/occasional/extra = 7 1 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (4)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) fix rheo/thermal, occasional, trim from (4)
|
||||
attributes: half, newton off, cut 3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(8) fix rheo/oxidation, perpetual, trim from (3)
|
||||
attributes: full, newton off, cut 1.8
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0 0 2701
|
||||
200 20 4.1743799e-07 1.1743617e-07 2701
|
||||
400 40 1.6697519e-06 4.6974469e-07 2701
|
||||
600 60 3.7127333e-06 1.0646825e-05 2701
|
||||
800 80 4.6683656e-06 0.00015182605 2701
|
||||
1000 100 4.7368707e-06 0.00028128761 2701
|
||||
1200 120 3.4384322e-06 0.00045913378 2701
|
||||
1400 140 1.4119866e-06 0.00055627091 2701
|
||||
1600 160 4.4114517e-07 0.00058247308 2701
|
||||
1800 180 4.8289229e-07 0.0005510948 2701
|
||||
2000 200 1.8494183e-06 0.00048386222 2701
|
||||
2200 220 3.3319816e-06 0.00037903264 2701
|
||||
2400 240 3.8128922e-06 0.00024115906 2701
|
||||
2600 260 3.1943401e-06 9.727407e-05 2701
|
||||
2800 280 1.6172816e-06 -2.632162e-05 2701
|
||||
3000 300 3.6100709e-07 -8.5761867e-05 2701
|
||||
3200 320 1.4745502e-07 -5.9204127e-05 2701
|
||||
3400 340 8.3369782e-07 8.8312464e-07 2701
|
||||
3600 360 2.0484052e-06 5.8521477e-05 2701
|
||||
3800 380 3.1639387e-06 0.0001685663 2701
|
||||
4000 400 3.1692907e-06 0.00026875988 2701
|
||||
4200 420 2.391933e-06 0.00038621787 2701
|
||||
4400 440 1.1964404e-06 0.00048901286 2701
|
||||
4600 460 4.0508824e-07 0.00051863639 2701
|
||||
4800 480 5.4908507e-07 0.00049263754 2701
|
||||
5000 500 1.3139665e-06 0.00041984264 2701
|
||||
5200 520 2.1939161e-06 0.00033095351 2701
|
||||
5400 540 2.3687031e-06 0.00022422981 2701
|
||||
5600 560 1.8280882e-06 0.00011544328 2701
|
||||
5800 580 8.8610517e-07 2.9307791e-05 2701
|
||||
6000 600 2.0989359e-07 -1.7340941e-05 2701
|
||||
6200 620 2.8658301e-07 -8.1237835e-06 2701
|
||||
6400 640 9.7636239e-07 4.3755922e-05 2701
|
||||
6600 660 1.891303e-06 0.0001185719 2701
|
||||
6800 680 2.4149904e-06 0.00020830273 2701
|
||||
7000 700 2.3174953e-06 0.00030114767 2701
|
||||
7200 720 1.7918612e-06 0.00037821537 2701
|
||||
7400 740 1.2114987e-06 0.0004233475 2701
|
||||
7600 760 9.9661553e-07 0.00042958263 2701
|
||||
7800 780 1.1552559e-06 0.00039944618 2701
|
||||
8000 800 1.5249138e-06 0.00034034478 2701
|
||||
8200 820 1.7453861e-06 0.00026826463 2701
|
||||
8400 840 1.6259021e-06 0.00019131768 2701
|
||||
8600 860 1.2612805e-06 0.0001162957 2701
|
||||
8800 880 8.6964518e-07 7.1771506e-05 2701
|
||||
9000 900 7.6892472e-07 5.6170687e-05 2701
|
||||
9200 920 1.0780045e-06 7.1925995e-05 2701
|
||||
9400 940 1.6514902e-06 0.00011635293 2701
|
||||
9600 960 2.1891377e-06 0.00017599885 2701
|
||||
9800 980 2.4551701e-06 0.00024127934 2701
|
||||
10000 1000 2.4277051e-06 0.00029918622 2701
|
||||
10200 1020 2.2655987e-06 0.00034067996 2701
|
||||
10400 1040 2.1767207e-06 0.00035598133 2701
|
||||
10600 1060 2.2796719e-06 0.00034359076 2701
|
||||
10800 1080 2.4884225e-06 0.00030749714 2701
|
||||
11000 1100 2.6387215e-06 0.00025725198 2701
|
||||
11200 1120 2.5968908e-06 0.00020170699 2701
|
||||
11400 1140 2.4108931e-06 0.00015185858 2701
|
||||
11600 1160 2.2375166e-06 0.00011800349 2701
|
||||
11800 1180 2.2407196e-06 0.00010646971 2701
|
||||
12000 1200 2.4845263e-06 0.00011817498 2701
|
||||
12200 1220 2.8733204e-06 0.00015013186 2701
|
||||
12400 1240 3.2437087e-06 0.00019211975 2701
|
||||
12600 1260 3.4732728e-06 0.00023620276 2701
|
||||
12800 1280 3.5836611e-06 0.00027352269 2701
|
||||
13000 1300 3.6592211e-06 0.00029533734 2701
|
||||
13200 1320 3.782506e-06 0.00030032559 2701
|
||||
13400 1340 3.9807086e-06 0.00028395722 2701
|
||||
13600 1360 4.2023176e-06 0.00025390325 2701
|
||||
13800 1380 4.3559781e-06 0.00021794236 2701
|
||||
14000 1400 4.4273371e-06 0.00018026034 2701
|
||||
14200 1420 4.49867e-06 0.0001526569 2701
|
||||
14400 1440 4.6591574e-06 0.00013707051 2701
|
||||
14600 1460 4.9589583e-06 0.00013803875 2701
|
||||
14800 1480 5.3859375e-06 0.00015455425 2701
|
||||
15000 1500 5.8639557e-06 0.00017954785 2701
|
||||
15200 1520 6.3075561e-06 0.0002084257 2701
|
||||
15400 1540 6.7022179e-06 0.0002347669 2701
|
||||
15600 1560 7.0789688e-06 0.00025020766 2701
|
||||
15800 1580 7.4734777e-06 0.00025394845 2701
|
||||
16000 1600 7.8884743e-06 0.00024571725 2701
|
||||
16200 1620 8.3224059e-06 0.00022706648 2701
|
||||
16400 1640 8.7337783e-06 0.00020320706 2701
|
||||
16600 1660 9.1454649e-06 0.00017824346 2701
|
||||
16800 1680 9.5948793e-06 0.00015961835 2701
|
||||
17000 1700 1.0106407e-05 0.00015135471 2701
|
||||
17200 1720 1.0707273e-05 0.00015166884 2701
|
||||
17400 1740 1.1392597e-05 0.0001645916 2701
|
||||
17600 1760 1.2118829e-05 0.00018119729 2701
|
||||
17800 1780 1.2846056e-05 0.0002003616 2701
|
||||
18000 1800 1.3555288e-05 0.00021585952 2701
|
||||
18200 1820 1.4301024e-05 0.00022290158 2701
|
||||
18400 1840 1.5089217e-05 0.00021970192 2701
|
||||
18600 1860 1.5902351e-05 0.00020911128 2701
|
||||
18800 1880 1.6753175e-05 0.00019278718 2701
|
||||
19000 1900 1.7602996e-05 0.00017584076 2701
|
||||
19200 1920 1.8479378e-05 0.00016206226 2701
|
||||
19400 1940 1.9421603e-05 0.00015575677 2701
|
||||
19600 1960 2.0477421e-05 0.00015687558 2701
|
||||
19800 1980 2.1617288e-05 0.00016424998 2701
|
||||
20000 2000 2.2814347e-05 0.00017466664 2701
|
||||
20200 2020 2.4029097e-05 0.00018647149 2701
|
||||
20400 2040 2.5255953e-05 0.00019516077 2701
|
||||
20600 2060 2.649418e-05 0.00019906384 2701
|
||||
20800 2080 2.7755897e-05 0.00019630586 2701
|
||||
21000 2100 2.9067854e-05 0.00018674721 2701
|
||||
21200 2120 3.0396477e-05 0.0001758048 2701
|
||||
21400 2140 3.1759719e-05 0.00016782801 2701
|
||||
21600 2160 3.3193597e-05 0.00016324138 2701
|
||||
21800 2180 3.4729384e-05 0.00016124274 2701
|
||||
22000 2200 3.6367594e-05 0.00016437457 2701
|
||||
22200 2220 3.8095131e-05 0.00017015573 2701
|
||||
22400 2240 3.9867003e-05 0.00017649465 2701
|
||||
22600 2260 4.169511e-05 0.00018111374 2701
|
||||
22800 2280 4.3566134e-05 0.00018104136 2701
|
||||
23000 2300 4.5461538e-05 0.00017822707 2701
|
||||
23200 2320 4.7377333e-05 0.00017285066 2701
|
||||
23400 2340 4.9354403e-05 0.00016826524 2701
|
||||
23600 2360 5.1399791e-05 0.00016517913 2701
|
||||
23800 2380 5.3510931e-05 0.00016299649 2701
|
||||
24000 2400 5.5681048e-05 0.00016256674 2701
|
||||
24200 2420 5.7902429e-05 0.00016513449 2701
|
||||
24400 2440 6.0216049e-05 0.00016895109 2701
|
||||
24600 2460 6.270982e-05 0.00016946227 2701
|
||||
24800 2480 6.5390117e-05 0.00016589426 2701
|
||||
25000 2500 6.8121899e-05 0.00016241676 2701
|
||||
25200 2520 7.0947331e-05 0.00015624292 2701
|
||||
25400 2540 7.4304148e-05 0.0001449537 2701
|
||||
25600 2560 7.7745077e-05 0.00013179658 2701
|
||||
25800 2580 8.0739829e-05 0.00013098838 2701
|
||||
26000 2600 8.3827874e-05 0.00014278841 2701
|
||||
26200 2620 8.7060677e-05 0.00015381649 2701
|
||||
26400 2640 9.0266508e-05 0.00016130999 2701
|
||||
26600 2660 9.3339049e-05 0.00016908268 2701
|
||||
26800 2680 9.6347013e-05 0.00016771087 2701
|
||||
27000 2700 9.9294711e-05 0.00016577315 2701
|
||||
27200 2720 0.00010230007 0.0001670893 2701
|
||||
27400 2740 0.00010547172 0.00016569077 2701
|
||||
27600 2760 0.00010872426 0.00016506303 2701
|
||||
27800 2780 0.00011201844 0.00016482702 2701
|
||||
28000 2800 0.00011532129 0.00016694886 2701
|
||||
28200 2820 0.00011869854 0.00016163005 2701
|
||||
28400 2840 0.00012209747 0.00015339281 2701
|
||||
28600 2860 0.00012549322 0.00014765883 2701
|
||||
28800 2880 0.00012898685 0.00014241765 2701
|
||||
29000 2900 0.00013259039 0.00014215724 2701
|
||||
29200 2920 0.00013628209 0.00014881155 2701
|
||||
29400 2940 0.00014001213 0.00015671333 2701
|
||||
29600 2960 0.00014379216 0.00016446215 2701
|
||||
29800 2980 0.00014764687 0.0001639602 2701
|
||||
30000 3000 0.00015142301 0.00015664816 2701
|
||||
30200 3020 0.00015496407 0.00015545099 2701
|
||||
30400 3040 0.00015797338 0.00015368625 2701
|
||||
30600 3060 0.00016042141 0.00015679918 2701
|
||||
30800 3080 0.00016244716 0.00016093678 2701
|
||||
31000 3100 0.00016202247 0.00016066954 2701
|
||||
31200 3120 0.0001613312 0.00015932059 2701
|
||||
31400 3140 0.00016274961 0.00015988567 2701
|
||||
31600 3160 0.00016541518 0.00015724809 2701
|
||||
31800 3180 0.00016809362 0.00015498827 2701
|
||||
32000 3200 0.00017067801 0.00014830489 2701
|
||||
32200 3220 0.00017333906 0.00014371345 2701
|
||||
32400 3240 0.0001759011 0.00014421259 2701
|
||||
32600 3260 0.00017849952 0.00014228443 2701
|
||||
32800 3280 0.00017801812 0.00014117391 2701
|
||||
33000 3300 0.00017718857 0.00014644675 2701
|
||||
33200 3320 0.00017833666 0.0001291286 2701
|
||||
33400 3340 0.000178576 0.00014878558 2701
|
||||
33600 3360 0.00017846711 0.00013905481 2701
|
||||
33800 3380 0.00017822937 0.00015535996 2701
|
||||
34000 3400 0.00017899663 0.00016094303 2701
|
||||
34200 3420 0.00017924661 0.00015017553 2701
|
||||
34400 3440 0.00018024855 0.00014723549 2701
|
||||
34600 3460 0.00018143865 0.00013903131 2701
|
||||
34800 3480 0.00018258173 0.00013722112 2701
|
||||
35000 3500 0.00018404873 0.00014675949 2701
|
||||
35200 3520 0.00018538521 0.00015108242 2701
|
||||
35400 3540 0.00018669649 0.00014564852 2701
|
||||
35600 3560 0.00018814608 0.00013762161 2701
|
||||
35800 3580 0.00018967415 0.00014602307 2701
|
||||
36000 3600 0.00019146735 0.000126909 2701
|
||||
36200 3620 0.00019414036 0.00012384379 2701
|
||||
36400 3640 0.00019613057 0.00011059573 2701
|
||||
36600 3660 0.00019897104 0.00013621801 2701
|
||||
36800 3680 0.00020169688 0.00013665462 2701
|
||||
37000 3700 0.00020447655 0.00013929258 2701
|
||||
37200 3720 0.00020711105 0.0001363895 2701
|
||||
37400 3740 0.00021077854 0.00013610672 2701
|
||||
37600 3760 0.00021303084 0.00015051235 2701
|
||||
37800 3780 0.00021619561 0.00012664801 2701
|
||||
38000 3800 0.0002194018 0.00012808247 2701
|
||||
38200 3820 0.00022242646 0.0001360174 2701
|
||||
38400 3840 0.00022531568 0.00013311221 2701
|
||||
38600 3860 0.00022821731 0.00013523939 2701
|
||||
38800 3880 0.000231228 0.00014090695 2701
|
||||
39000 3900 0.00023404038 0.00013661835 2701
|
||||
39200 3920 0.00023755044 0.00013659469 2701
|
||||
39400 3940 0.00024009059 0.00012097907 2701
|
||||
39600 3960 0.0002432098 9.7877876e-05 2701
|
||||
39800 3980 0.00024475294 0.0001164688 2701
|
||||
40000 4000 0.00024171274 0.00012432219 2701
|
||||
Loop time of 192.659 on 4 procs for 40000 steps with 2701 atoms
|
||||
|
||||
Performance: 1793840.118 tau/day, 207.620 timesteps/s, 560.783 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.881 | 24.402 | 30.74 | 114.6 | 12.67
|
||||
Bond | 1.1126 | 1.8917 | 2.6935 | 43.3 | 0.98
|
||||
Neigh | 35.387 | 35.508 | 35.625 | 1.5 | 18.43
|
||||
Comm | 1.5499 | 1.6694 | 1.8006 | 7.4 | 0.87
|
||||
Output | 0.99755 | 1.0072 | 1.0165 | 0.8 | 0.52
|
||||
Modify | 120.6 | 127.43 | 135.54 | 54.8 | 66.14
|
||||
Other | | 0.7553 | | | 0.39
|
||||
|
||||
Nlocal: 675.25 ave 1373 max 7 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 103 ave 163 max 50 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 10509 ave 21592 max 126 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 20367 ave 41981 max 141 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 81468
|
||||
Ave neighs/atom = 30.162162
|
||||
Ave special neighs/atom = 1.6593854
|
||||
Neighbor list builds = 39932
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:03:12
|
||||
75
examples/rheo/poiseuille/in.rheo.poiseuille
Normal file
75
examples/rheo/poiseuille/in.rheo.poiseuille
Normal file
@ -0,0 +1,75 @@
|
||||
# ------ 2D Poiseuille flow ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 20 -10 10 -0.01 0.01
|
||||
create_box 2 box
|
||||
lattice sq ${n}
|
||||
|
||||
region inner block INF INF -7.5 7.5 INF INF units box
|
||||
region walls block INF INF -7.5 7.5 INF INF units box side out
|
||||
|
||||
create_atoms 2 region walls
|
||||
create_atoms 1 region inner
|
||||
|
||||
group fluid type 1
|
||||
group rig type 2
|
||||
|
||||
displace_atoms fluid random 0.1 0.1 0 135414 units box
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 1.0
|
||||
variable kappa equal 1.0*${rho0}/${mp}
|
||||
variable fext equal 1e-4/${n}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable Dr equal 0.05*${cut}*${cs}
|
||||
|
||||
variable eta equal 0.1
|
||||
variable gd0 equal 5e-4
|
||||
variable npow equal 0.5
|
||||
variable K equal 0.001
|
||||
|
||||
mass * ${mp}
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/status 0
|
||||
set group rig rheo/status 1
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
#fix 2 all rheo/viscosity * power ${eta} ${gd0} ${K} ${npow}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 rig setforce 0.0 0.0 0.0
|
||||
fix 5 fluid addforce ${fext} 0.0 0.0
|
||||
fix 6 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 20000
|
||||
|
||||
288
examples/rheo/poiseuille/log.17Apr2024.poiseuille.g++.4
Normal file
288
examples/rheo/poiseuille/log.17Apr2024.poiseuille.g++.4
Normal file
@ -0,0 +1,288 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D Poiseuille flow ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 20 -10 10 -0.01 0.01
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
lattice sq ${n}
|
||||
lattice sq 1
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
|
||||
region inner block INF INF -7.5 7.5 INF INF units box
|
||||
region walls block INF INF -7.5 7.5 INF INF units box side out
|
||||
|
||||
create_atoms 2 region walls
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 region inner
|
||||
Created 300 atoms
|
||||
using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
group fluid type 1
|
||||
300 atoms in group fluid
|
||||
group rig type 2
|
||||
100 atoms in group rig
|
||||
|
||||
displace_atoms fluid random 0.1 0.1 0 135414 units box
|
||||
Displacing atoms ...
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 1.0
|
||||
variable kappa equal 1.0*${rho0}/${mp}
|
||||
variable kappa equal 1.0*1/${mp}
|
||||
variable kappa equal 1.0*1/1
|
||||
variable fext equal 1e-4/${n}
|
||||
variable fext equal 1e-4/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable Dr equal 0.05*${cut}*${cs}
|
||||
variable Dr equal 0.05*3*${cs}
|
||||
variable Dr equal 0.05*3*1
|
||||
|
||||
variable eta equal 0.1
|
||||
variable gd0 equal 5e-4
|
||||
variable npow equal 0.5
|
||||
variable K equal 0.001
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/rho 1
|
||||
Setting atom values ...
|
||||
400 settings made for rheo/rho
|
||||
set group all rheo/status 0
|
||||
Setting atom values ...
|
||||
400 settings made for rheo/status
|
||||
set group rig rheo/status 1
|
||||
Setting atom values ...
|
||||
100 settings made for rheo/status
|
||||
|
||||
timestep ${dt_max}
|
||||
timestep 0.1
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp 0.15
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift
|
||||
fix 1 all rheo 3 quintic 0 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.1
|
||||
#fix 2 all rheo/viscosity * power ${eta} ${gd0} ${K} ${npow}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 rig setforce 0.0 0.0 0.0
|
||||
fix 5 fluid addforce ${fext} 0.0 0.0
|
||||
fix 5 fluid addforce 0.0001 0.0 0.0
|
||||
fix 6 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 20000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 13 13 1
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair rheo, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.693 | 5.693 | 5.693 Mbytes
|
||||
Step Time KinEng Press
|
||||
0 0 0 0
|
||||
200 20 1.2220462e-06 3.7383146e-05
|
||||
400 40 4.345762e-06 7.5866885e-05
|
||||
600 60 8.8559433e-06 0.00011353743
|
||||
800 80 1.4370506e-05 0.00015135634
|
||||
1000 100 2.0576198e-05 0.00018903722
|
||||
1200 120 2.721926e-05 0.00022533997
|
||||
1400 140 3.4099653e-05 0.00026016069
|
||||
1600 160 4.1064175e-05 0.00029445207
|
||||
1800 180 4.8001225e-05 0.00032893763
|
||||
2000 200 5.4832849e-05 0.00036402396
|
||||
2200 220 6.1508431e-05 0.00039945249
|
||||
2400 240 6.8000141e-05 0.00043534411
|
||||
2600 260 7.430136e-05 0.00046943441
|
||||
2800 280 8.0415328e-05 0.00049807225
|
||||
3000 300 8.6335032e-05 0.00051815375
|
||||
3200 320 9.2021626e-05 0.00052618224
|
||||
3400 340 9.7387936e-05 0.00051877918
|
||||
3600 360 0.00010231526 0.00048650828
|
||||
3800 380 0.00010676617 0.00044578079
|
||||
4000 400 0.00011080098 0.00044777126
|
||||
4200 420 0.00011448127 0.00047047629
|
||||
4400 440 0.00011787852 0.00050280249
|
||||
4600 460 0.00012106805 0.0005397213
|
||||
4800 480 0.00012412056 0.00057885539
|
||||
5000 500 0.0001271078 0.00061396896
|
||||
5200 520 0.00013006637 0.00063981812
|
||||
5400 540 0.00013295039 0.00065094073
|
||||
5600 560 0.00013561487 0.00063918847
|
||||
5800 580 0.00013791796 0.00059087656
|
||||
6000 600 0.00013983422 0.00052171998
|
||||
6200 620 0.00014144833 0.00050658002
|
||||
6400 640 0.00014286538 0.0005248626
|
||||
6600 660 0.00014417734 0.00055826606
|
||||
6800 680 0.00014546931 0.00060063748
|
||||
7000 700 0.00014682553 0.00064421411
|
||||
7200 720 0.0001482833 0.00068252242
|
||||
7400 740 0.00014977996 0.00070671308
|
||||
7600 760 0.00015114829 0.00069774026
|
||||
7800 780 0.0001522719 0.00064408311
|
||||
8000 800 0.00015312897 0.00055977044
|
||||
8200 820 0.00015375669 0.0005225573
|
||||
8400 840 0.00015425683 0.00053833691
|
||||
8600 860 0.00015471278 0.00057447427
|
||||
8800 880 0.0001552059 0.00061980921
|
||||
9000 900 0.00015581593 0.0006659836
|
||||
9200 920 0.0001565564 0.00070813532
|
||||
9400 940 0.00015733573 0.00073378551
|
||||
9600 960 0.00015802107 0.00071560835
|
||||
9800 980 0.00015855339 0.00065636189
|
||||
10000 1000 0.00015890743 0.0005699855
|
||||
10200 1020 0.00015908095 0.00053138971
|
||||
10400 1040 0.00015915523 0.00054790708
|
||||
10600 1060 0.00015921254 0.00058899454
|
||||
10800 1080 0.00015934193 0.00063964906
|
||||
11000 1100 0.00015959891 0.00069241358
|
||||
11200 1120 0.0001599636 0.00073734651
|
||||
11400 1140 0.00016036526 0.00074477329
|
||||
11600 1160 0.00016075471 0.00071047555
|
||||
11800 1180 0.00016109516 0.00064173183
|
||||
12000 1200 0.00016131524 0.00055500553
|
||||
12200 1220 0.00016136366 0.0005290215
|
||||
12400 1240 0.0001613025 0.00055124296
|
||||
12600 1260 0.00016123023 0.00059758627
|
||||
12800 1280 0.00016123043 0.00065488735
|
||||
13000 1300 0.00016132935 0.0007140876
|
||||
13200 1320 0.00016152165 0.00074795629
|
||||
13400 1340 0.00016180372 0.00074730778
|
||||
13600 1360 0.00016216585 0.00071370995
|
||||
13800 1380 0.0001625339 0.00065176323
|
||||
14000 1400 0.00016274999 0.00057515371
|
||||
14200 1420 0.00016271295 0.00055878258
|
||||
14400 1440 0.00016249768 0.00058448193
|
||||
14600 1460 0.00016223675 0.00063096229
|
||||
14800 1480 0.00016201846 0.00068639548
|
||||
15000 1500 0.00016190593 0.00072444357
|
||||
15200 1520 0.00016194466 0.00073830636
|
||||
15400 1540 0.00016216164 0.00072773256
|
||||
15600 1560 0.00016253174 0.00069215481
|
||||
15800 1580 0.00016290895 0.00063239408
|
||||
16000 1600 0.00016306463 0.00057466273
|
||||
16200 1620 0.00016292218 0.00057951567
|
||||
16400 1640 0.00016261117 0.00061504156
|
||||
16600 1660 0.00016225906 0.00066066637
|
||||
16800 1680 0.00016197993 0.00069751908
|
||||
17000 1700 0.0001618568 0.00072202303
|
||||
17200 1720 0.00016194264 0.00073255034
|
||||
17400 1740 0.00016225911 0.0007231031
|
||||
17600 1760 0.00016270465 0.00068931224
|
||||
17800 1780 0.00016304053 0.00062934836
|
||||
18000 1800 0.00016302624 0.00058060272
|
||||
18200 1820 0.00016274847 0.00058859513
|
||||
18400 1840 0.00016236893 0.00061804803
|
||||
18600 1860 0.00016202777 0.00065393237
|
||||
18800 1880 0.0001618184 0.00068747094
|
||||
19000 1900 0.0001618044 0.00071352541
|
||||
19200 1920 0.00016204402 0.00072351769
|
||||
19400 1940 0.00016249999 0.00071330322
|
||||
19600 1960 0.00016297924 0.00067984167
|
||||
19800 1980 0.00016317435 0.00061634142
|
||||
20000 2000 0.00016301186 0.00057234115
|
||||
Loop time of 15.6198 on 4 procs for 20000 steps with 400 atoms
|
||||
|
||||
Performance: 11062881.511 tau/day, 1280.426 timesteps/s, 512.170 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1979 | 2.4473 | 2.6992 | 15.7 | 15.67
|
||||
Neigh | 0.024709 | 0.027006 | 0.029223 | 1.3 | 0.17
|
||||
Comm | 0.4657 | 0.71686 | 0.9662 | 29.0 | 4.59
|
||||
Output | 0.033698 | 0.036781 | 0.039359 | 1.1 | 0.24
|
||||
Modify | 12.306 | 12.313 | 12.319 | 0.2 | 78.83
|
||||
Other | | 0.07916 | | | 0.51
|
||||
|
||||
Nlocal: 100 ave 107 max 93 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 185.5 ave 192 max 179 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1712 ave 1848 max 1598 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
FullNghs: 3424 ave 3682 max 3174 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 13696
|
||||
Ave neighs/atom = 34.24
|
||||
Neighbor list builds = 331
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:15
|
||||
65
examples/rheo/taylor-green/in.rheo.taylor.green
Normal file
65
examples/rheo/taylor-green/in.rheo.taylor.green
Normal file
@ -0,0 +1,65 @@
|
||||
# ------ 2D Taylor Green vortex ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 40 0 40 -0.01 0.01
|
||||
create_box 1 box
|
||||
lattice sq ${n}
|
||||
|
||||
create_atoms 1 region box
|
||||
|
||||
displace_atoms all random 0.1 0.1 0 135414 units box
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable cs equal 1.0
|
||||
variable eta equal 0.05
|
||||
variable zeta equal 1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable Dr equal 0.1*${cut}*${cs}
|
||||
|
||||
mass * ${mp}
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/status 0
|
||||
|
||||
variable u0 equal 0.05
|
||||
variable uy atom ${u0}*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||
variable ux atom -${u0}*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||
variable d0 atom ${rho0}-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
|
||||
velocity all set v_ux v_uy 0.0 units box
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} RK1 8 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 10000
|
||||
224
examples/rheo/taylor-green/log.17Apr2024.taylor.green.g++.4
Normal file
224
examples/rheo/taylor-green/log.17Apr2024.taylor.green.g++.4
Normal file
@ -0,0 +1,224 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D Taylor Green vortex ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 40 0 40 -0.01 0.01
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.01) to (40 40 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
lattice sq ${n}
|
||||
lattice sq 1
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
|
||||
create_atoms 1 region box
|
||||
Created 1600 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.01) to (40 40 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0 135414 units box
|
||||
Displacing atoms ...
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable cs equal 1.0
|
||||
variable eta equal 0.05
|
||||
variable zeta equal 1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable Dr equal 0.1*${cut}*${cs}
|
||||
variable Dr equal 0.1*3*${cs}
|
||||
variable Dr equal 0.1*3*1
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/rho 1
|
||||
Setting atom values ...
|
||||
1600 settings made for rheo/rho
|
||||
set group all rheo/status 0
|
||||
Setting atom values ...
|
||||
1600 settings made for rheo/status
|
||||
|
||||
variable u0 equal 0.05
|
||||
variable uy atom ${u0}*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||
variable uy atom 0.05*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||
variable ux atom -${u0}*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||
variable ux atom -0.05*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||
variable d0 atom ${rho0}-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*0.05*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/${cs}
|
||||
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/1
|
||||
|
||||
velocity all set v_ux v_uy 0.0 units box
|
||||
|
||||
timestep ${dt_max}
|
||||
timestep 0.1
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp 0.3
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} RK1 8 shift
|
||||
fix 1 all rheo 3 RK1 8 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 25 25 1
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair rheo, perpetual, half/full from (2)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.835 | 6.835 | 6.835 Mbytes
|
||||
Step Time KinEng Press
|
||||
0 0 0.00062497276 0.00062607301
|
||||
200 20 0.00056200647 0.00056633785
|
||||
400 40 0.00050570968 0.00051098771
|
||||
600 60 0.00045586684 0.00046081672
|
||||
800 80 0.00041124523 0.00041549607
|
||||
1000 100 0.00037065341 0.00037412741
|
||||
1200 120 0.00033391585 0.00033580899
|
||||
1400 140 0.00030078316 0.00030057307
|
||||
1600 160 0.00027093231 0.00026842603
|
||||
1800 180 0.00024403239 0.00023839026
|
||||
2000 200 0.0002197865 0.00021148941
|
||||
2200 220 0.0001979269 0.00018659386
|
||||
2400 240 0.00017822267 0.00016430442
|
||||
2600 260 0.00016047141 0.00014408514
|
||||
2800 280 0.00014448504 0.00012574125
|
||||
3000 300 0.00013009159 0.00010869938
|
||||
3200 320 0.00011713578 9.414951e-05
|
||||
3400 340 0.00010547564 8.1900579e-05
|
||||
3600 360 9.4982139e-05 7.1285649e-05
|
||||
3800 380 8.5538983e-05 6.1571123e-05
|
||||
4000 400 7.7040171e-05 5.3462572e-05
|
||||
4200 420 6.9390317e-05 4.6338308e-05
|
||||
4400 440 6.2503763e-05 3.9697323e-05
|
||||
4600 460 5.6303766e-05 3.4234465e-05
|
||||
4800 480 5.0721595e-05 3.0841338e-05
|
||||
5000 500 4.5695301e-05 2.7788566e-05
|
||||
5200 520 4.1169161e-05 2.5744409e-05
|
||||
5400 540 3.7093059e-05 2.3912739e-05
|
||||
5600 560 3.3421819e-05 2.2494185e-05
|
||||
5800 580 3.0114735e-05 2.1594384e-05
|
||||
6000 600 2.7135224e-05 2.1164421e-05
|
||||
6200 620 2.4450446e-05 2.0979349e-05
|
||||
6400 640 2.2030925e-05 2.0858567e-05
|
||||
6600 660 1.9850196e-05 2.098115e-05
|
||||
6800 680 1.7884553e-05 2.1134827e-05
|
||||
7000 700 1.6112763e-05 2.1242242e-05
|
||||
7200 720 1.4515783e-05 2.1312763e-05
|
||||
7400 740 1.3076456e-05 2.1370947e-05
|
||||
7600 760 1.1779327e-05 2.1332126e-05
|
||||
7800 780 1.0610469e-05 2.1156562e-05
|
||||
8000 800 9.5573298e-06 2.0898126e-05
|
||||
8200 820 8.6085799e-06 2.0517958e-05
|
||||
8400 840 7.7539888e-06 1.9841551e-05
|
||||
8600 860 6.9843033e-06 1.9114769e-05
|
||||
8800 880 6.2911575e-06 1.8362959e-05
|
||||
9000 900 5.6669785e-06 1.7473404e-05
|
||||
9200 920 5.1049208e-06 1.6452745e-05
|
||||
9400 940 4.5987908e-06 1.5578629e-05
|
||||
9600 960 4.1429972e-06 1.4427274e-05
|
||||
9800 980 3.7324962e-06 1.3169649e-05
|
||||
10000 1000 3.3627455e-06 1.1938723e-05
|
||||
Loop time of 38.2006 on 4 procs for 10000 steps with 1600 atoms
|
||||
|
||||
Performance: 2261743.875 tau/day, 261.776 timesteps/s, 418.841 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.2958 | 8.7273 | 9.3582 | 15.2 | 22.85
|
||||
Neigh | 0.034282 | 0.035689 | 0.037115 | 0.7 | 0.09
|
||||
Comm | 0.16788 | 0.17018 | 0.17278 | 0.4 | 0.45
|
||||
Output | 0.066977 | 0.06882 | 0.071704 | 0.7 | 0.18
|
||||
Modify | 28.483 | 28.793 | 28.962 | 3.6 | 75.37
|
||||
Other | | 0.4053 | | | 1.06
|
||||
|
||||
Nlocal: 400 ave 402 max 399 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 307.25 ave 308 max 305 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 7618.25 ave 7697 max 7564 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
FullNghs: 13343 ave 13497 max 13258 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 53372
|
||||
Ave neighs/atom = 33.3575
|
||||
Neighbor list builds = 123
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:38
|
||||
Reference in New Issue
Block a user