diff --git a/README.md b/README.md index 96123f4e7..f1cb3de75 100644 --- a/README.md +++ b/README.md @@ -80,6 +80,8 @@ The `System` or `LabeledSystem` can be constructed from the following file forma | Amber | multi | True | True | LabeledSystem | 'amber/md' | | Amber/sqm | sqm.out | False | False | System | 'sqm/out' | | Gromacs | gro | True | False | System | 'gromacs/gro' | +| ABACUS | STRU | False | True | LabeledSystem | 'abacus/scf' | +| ABACUS | cif | True | True | LabeledSystem | 'abacus/md' | The Class `dpdata.MultiSystems` can read data from a dir which may contains many files of different systems, or from single xyz file which contains different systems. diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py new file mode 100644 index 000000000..ebef4d8b1 --- /dev/null +++ b/dpdata/abacus/md.py @@ -0,0 +1,190 @@ +import os,sys +import numpy as np +from .scf import ry2ev, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords + +# Read in geometries from an ABACUS MD trajectory. +# The atomic coordinates are read in from generated files in OUT.XXXX. +# Energies, forces +# IMPORTANT: the program defaultly takes STRU input file as standard cell information, +# therefore the direct and cartesan coordinates read could be different from the ones in +# the output cif files!!! +# It is highly recommanded to use ORTHOGANAL coordinates in STRU file if you wish to get +# same coordinates in both dpdata and output cif files. + +def get_path_out(fname, inlines): + # This function is different from the same-name function in scf.py. + # This function returns OUT.XXXX's base directory. + path_out = os.path.join(fname, "OUT.ABACUS/") + for line in inlines: + if len(line)>0 and "suffix" in line and "suffix"==line.split()[0]: + suffix = line.split()[1] + path_out = os.path.join(fname, "OUT.%s/" % suffix) + break + return path_out + +def get_coord_dump_freq(inlines): + for line in inlines: + if len(line)>0 and "md_dumpmdfred" in line and "md_dumpmdfred" == line.split()[0]: + return int(line.split()[1]) + return 1 + +# set up a cell according to cell info in cif file. +# maybe useful later +''' +def setup_cell(a, b, c, alpha, beta, gamma): + cell = np.zeros(3, 3) + cell[0, 0] = a + cell[1, 0] = b*np.cos(gamma/180*np.pi) + cell[1, 1] = b*np.sin(gamma/180*np.pi) + cell[2, 0] = c*np.cos(beta/180*np.pi) + cell[2, 1] = c*(b*np.cos(alpha/180*np.pi) - cell[1, 0]*np.cos(beta/180*np.pi))/cell[1, 1] + cell[2, 2] = np.sqrt(c**2 - cell[2, 0]**2 - cell[2, 1]**2) + return cell +''' + +def get_single_coord_from_cif(pos_file, atom_names, natoms, cell): + assert(len(atom_names) == len(natoms)) + nele = len(atom_names) + total_natoms = sum(natoms) + coord = np.zeros([total_natoms, 3]) + a = 0 + b = 0 + c = 0 + alpha = 0 + beta = 0 + gamma = 0 + with open(pos_file, "r") as fp: + lines = fp.read().split("\n") + for line in lines: + if "_cell_length_a" in line: + a = float(line.split()[1]) + if "_cell_length_b" in line: + b = float(line.split()[1]) + if "_cell_length_c" in line: + c = float(line.split()[1]) + if "_cell_angle_alpha" in line: + alpha = float(line.split()[1]) + if "_cell_angle_beta" in line: + beta = float(line.split()[1]) + if "_cell_angle_gamma" in line: + gamma = float(line.split()[1]) + assert(a > 0 and b > 0 and c > 0 and alpha > 0 and beta > 0 and gamma > 0) + #cell = setup_cell(a, b, c, alpha, beta, gamma) + coord_lines = get_block(lines=lines, keyword="_atom_site_fract_z", skip=0, nlines = total_natoms) + + ia_idx = 0 + for it in range(nele): + for ia in range(natoms[it]): + coord_line = coord_lines[ia_idx].split() + assert(coord_line[0] == atom_names[it]) + coord[ia_idx, 0] = float(coord_line[1]) + coord[ia_idx, 1] = float(coord_line[2]) + coord[ia_idx, 2] = float(coord_line[3]) + ia_idx+=1 + coord = np.matmul(coord, cell) + # important! Coordinates are converted to Cartesian coordinate. + return coord + + +def get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell): + total_natoms = sum(natoms) + #cell = np.zeros(ndump, 3, 3) + coords = np.zeros([ndump, total_natoms, 3]) + pos_file = os.path.join(path_out, "STRU_READIN_ADJUST.cif") + # frame 0 file is different from any other frames + coords[0] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) + for dump_idx in range(1, ndump): + pos_file = os.path.join(path_out, "md_pos_%d.cif" %(dump_idx*dump_freq)) + #print("dump_idx = %s" %dump_idx) + coords[dump_idx] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) + return coords + +def get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names): + stress = None + total_natoms = sum(natoms) + for line in inlines: + if len(line)>0 and "stress" in line and "stress" == line.split()[0] and "1" == line.split()[1]: + stress = np.zeros([ndump, 3, 3]) + break + if type(stress) != np.ndarray: + print("The ABACUS program has no stress output. Stress will not be read.") + nenergy = 0 + nforce = 0 + nstress = 0 + energy = np.zeros(ndump) + force = np.zeros([ndump, total_natoms, 3]) + + for line_idx, line in enumerate(outlines): + if "final etot is" in line: + if nenergy%dump_freq == 0: + energy[int(nenergy/dump_freq)] = float(line.split()[-2]) + nenergy+=1 + if "TOTAL-FORCE (eV/Angstrom)" in line: + for iatom in range(0, total_natoms): + force_line = outlines[line_idx+5+iatom] + atom_force = [float(i) for i in force_line.split()[1:]] + assert(len(atom_force) == 3) + atom_force = np.array(atom_force) + if nforce%dump_freq == 0: + force[int(nforce/dump_freq), iatom] = atom_force + nforce+=1 + assert(nforce==nenergy) + if "TOTAL-STRESS (KBAR)" in line: + for idx in range(0, 3): + stress_line = outlines[line_idx+4+idx] + single_stress = [float(i) for i in stress_line.split()] + if len(single_stress) != 3: + print(single_stress) + assert(len(single_stress) == 3) + single_stress = np.array(single_stress) + if nstress%dump_freq == 0: + stress[int(nstress/dump_freq), idx] = single_stress + nstress+=1 + assert(nstress==nforce) + if type(stress) == np.ndarray: + stress *= kbar2evperang3 + return energy, force, stress + + +def get_frame (fname): + if type(fname) == str: + # if the input parameter is only one string, it is assumed that it is the + # base directory containing INPUT file; + path_in = os.path.join(fname, "INPUT") + else: + raise RuntimeError('invalid input') + with open(path_in, 'r') as fp: + inlines = fp.read().split('\n') + geometry_path_in = get_geometry_in(fname, inlines) # base dir of STRU + path_out = get_path_out(fname, inlines) + + with open(geometry_path_in, 'r') as fp: + geometry_inlines = fp.read().split('\n') + celldm, cell = get_cell(geometry_inlines) + atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) + # This coords is not to be used. + dump_freq = get_coord_dump_freq(inlines = inlines) + ndump = int(os.popen("ls --l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0]) + # number of dumped geometry files + coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell) + + # TODO: Read in energies, forces and pressures. + with open(os.path.join(path_out, "running_md.log"), 'r') as fp: + outlines = fp.read().split('\n') + energy, force, stress = get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names) + if type(stress) == np.ndarray: + stress *= np.linalg.det(cell) + data = {} + data['atom_names'] = atom_names + data['atom_numbs'] = natoms + data['atom_types'] = types + data['cells'] = np.zeros([ndump, 3, 3]) + for idx in range(ndump): + data['cells'][:, :, :] = cell + data['coords'] = coords + data['energies'] = energy + data['forces'] = force + data['virials'] = stress + data['orig'] = np.zeros(3) + + return data diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py index 531837ef8..41dd40a70 100644 --- a/dpdata/abacus/scf.py +++ b/dpdata/abacus/scf.py @@ -174,6 +174,6 @@ def get_frame (fname): # print("virial = ", data['virials']) return data -if __name__ == "__main__": - path = "/home/lrx/work/12_ABACUS_dpgen_interface/dpdata/dpdata/tests/abacus.scf" - data = get_frame(path) \ No newline at end of file +#if __name__ == "__main__": +# path = "/home/lrx/work/12_ABACUS_dpgen_interface/dpdata/dpdata/tests/abacus.scf" +# data = get_frame(path) \ No newline at end of file diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py index ad37cdfa2..43403772a 100644 --- a/dpdata/plugins/abacus.py +++ b/dpdata/plugins/abacus.py @@ -1,10 +1,19 @@ import dpdata.abacus.scf +import dpdata.abacus.md from dpdata.format import Format @Format.register("abacus/scf") @Format.register("abacus/pw/scf") class AbacusSCFFormat(Format): - @Format.post("rot_lower_triangular") + #@Format.post("rot_lower_triangular") def from_labeled_system(self, file_name, **kwargs): return dpdata.abacus.scf.get_frame(file_name) + +@Format.register("abacus/md") +@Format.register("abacus/pw/md") +@Format.register("abacus/lcao/md") +class AbacusMDFormat(Format): + #@Format.post("rot_lower_triangular") + def from_labeled_system(self, file_name, **kwargs): + return dpdata.abacus.md.get_frame(file_name) diff --git a/dpdata/system.py b/dpdata/system.py index 00185b1a6..72c6c1bad 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -76,7 +76,8 @@ def __init__ (self, - ``vasp/poscar``: vasp POSCAR - ``qe/cp/traj``: Quantum Espresso CP trajectory files. should have: file_name+'.in' and file_name+'.pos' - ``qe/pw/scf``: Quantum Espresso PW single point calculations. Both input and output files are required. If file_name is a string, it denotes the output file name. Input file name is obtained by replacing 'out' by 'in' from file_name. Or file_name is a list, with the first element being the input file name and the second element being the output filename. - - ``abacus/scf``: ABACUS plane wave scf. The directory containing INPUT file is required. + - ``abacus/scf``: ABACUS pw/lcao scf. The directory containing INPUT file is required. + - ``abacus/md``: ABACUS pw/lcao MD. The directory containing INPUT file is required. - ``siesta/output``: siesta SCF output file - ``siesta/aimd_output``: siesta aimd output file - ``pwmat/atom.config``: pwmat atom.config diff --git a/tests/abacus.md/INPUT b/tests/abacus.md/INPUT new file mode 100644 index 000000000..d169ddf95 --- /dev/null +++ b/tests/abacus.md/INPUT @@ -0,0 +1,30 @@ +INPUT_PARAMETERS +#Parameters (General) +suffix autotest +pseudo_dir ./ +ntype 1 +nbands 8 +calculation md +read_file_dir ./ + +#Parameters (Accuracy) +ecutwfc 20 +niter 20 + +basis_type pw +nstep 21 # number of MD/relaxation steps + +stress 1 +stress_thr 1e-6 +force 1 +force_thr_ev 1.0e-3 + +ks_solver cg +mixing_type pulay +mixing_beta 0.7 + +md_mdtype 1 # 0 for NVE; 1 for NVT with Nose Hoover; 2 for NVT with velocity rescaling +md_tfirst 10 # temperature, unit: K +md_dt 1 # unit: fs +md_rstmd 0 # 1 for restart +md_dumpmdfred 5 diff --git a/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif b/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif new file mode 100644 index 000000000..24779f6c0 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0 0 0 +Si 0.245 0.237 0.265 diff --git a/tests/abacus.md/OUT.autotest/md_pos_1.cif b/tests/abacus.md/OUT.autotest/md_pos_1.cif new file mode 100644 index 000000000..832aaef0a --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_1.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.00106888 0.99849 0.000247409 +Si 0.245535 0.237394 0.262886 diff --git a/tests/abacus.md/OUT.autotest/md_pos_10.cif b/tests/abacus.md/OUT.autotest/md_pos_10.cif new file mode 100644 index 000000000..a7546cea6 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_10.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.00711478 0.993904 0.9916 +Si 0.253316 0.23197 0.255312 diff --git a/tests/abacus.md/OUT.autotest/md_pos_15.cif b/tests/abacus.md/OUT.autotest/md_pos_15.cif new file mode 100644 index 000000000..51f15b4ea --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_15.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.00722617 0.979891 0.000667301 +Si 0.260608 0.240666 0.237553 diff --git a/tests/abacus.md/OUT.autotest/md_pos_20.cif b/tests/abacus.md/OUT.autotest/md_pos_20.cif new file mode 100644 index 000000000..3d01862a9 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_20.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.0136053 0.987589 0.984304 +Si 0.261345 0.227707 0.245529 diff --git a/tests/abacus.md/OUT.autotest/md_pos_5.cif b/tests/abacus.md/OUT.autotest/md_pos_5.cif new file mode 100644 index 000000000..b35b1102d --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_5.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.999048 0.984501 0.010401 +Si 0.2538 0.246892 0.24541 diff --git a/tests/abacus.md/OUT.autotest/running_md.log b/tests/abacus.md/OUT.autotest/running_md.log new file mode 100644 index 000000000..16f460507 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/running_md.log @@ -0,0 +1,2608 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 1 + Start Time is Fri Oct 15 14:37:16 2021 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.autotest/ + global_in_card = INPUT + pseudo_dir = ./ + orbital_dir = ./ + pseudo_type = auto + DRANK = 1 + DSIZE = 1 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 1 + atom label for species 1 = Si + lattice constant (Bohr) = 10.2 + lattice constant (Angstrom) = 5.39761 + + READING ATOM TYPE 1 + atom label = Si + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 2 + + CARTESIAN COORDINATES ( UNIT = 10.2 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0 0 0 0 0 0 0 + tauc_Si2 0.241 0.255 0.250999999999 0 0 0 0 + + + Volume (Bohr^3) = 265.302 + Volume (A^3) = 39.3136533177 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +0.5 +0.5 +0 + +0.5 +0 +0.5 + +0 +0.5 +0.5 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +1 +1 -1 + +1 -1 +1 + -1 +1 +1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./Si_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + initial pseudo atomic orbital number = 0 + NLOCAL = 18 + + SETUP THE ELECTRONS NUMBER + electron number of element Si = 4 + total electron number of element Si = 8 + occupied bands = 4 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0648149461485 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 8 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 0.125 + 2 0.5 0 0 0.125 + 3 0 0.5 0 0.125 + 4 0.5 0.5 0 0.125 + 5 0 0 0.5 0.125 + 6 0.5 0 0.5 0.125 + 7 0 0.5 0.5 0.125 + 8 0.5 0.5 0.5 0.125 + + k-point number in this process = 8 + minimum distributed K point number = 8 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 0.25 + 2 0.5 0.5 -0.5 0.25 + 3 0.5 -0.5 0.5 0.25 + 4 1 0 0 0.25 + 5 -0.5 0.5 0.5 0.25 + 6 0 1 0 0.25 + 7 0 0 1 0.25 + 8 0.5 0.5 0.5 0.25 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 0.25 + 2 0.5 0 0 0.25 + 3 0 0.5 0 0.25 + 4 0.5 0.5 0 0.25 + 5 0 0 0.5 0.25 + 6 0.5 0 0.5 0.25 + 7 0 0.5 0.5 0.25 + 8 0.5 0.5 0.5 0.25 + DONE : INIT K-POINTS Time : 0.0652149026282 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for wavefunc (unit:Ry) = 20 + [fft grid for wave functions] = 24, 24, 24 + [fft grid for charge/potential] = 24, 24, 24 + [fft grid division] = 1, 1, 1 + [big fft grid for charge/potential] = 24, 24, 24 + nbxx = 13824 + nrxx = 13824 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 3143 + number of sticks = 283 + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + number of plane waves = 609 + number of sticks = 91 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 283 3143 + --------------- sum ------------------- + 1 283 3143 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(W) PW + 1 91 609 + --------------- sum ------------------- + 1 91 609 + + SETUP COORDINATES OF PLANE WAVES + number of total plane waves = 3143 + + SETUP COORDINATES OF PLANE WAVES + number of |g| = 72 + max |g| = 208 + min |g| = 0 + DONE : INIT PLANEWAVE Time : 0.0986429497134 (SEC) + + npwx = 411 + + SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS + Si non-local projectors: + projector 1 L=0 + projector 2 L=0 + projector 3 L=1 + projector 4 L=1 + TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 + DONE : LOCAL POTENTIAL Time : 0.109992648242 (SEC) + + + Init Non-Local PseudoPotential table : + Init Non-Local-Pseudopotential done. + DONE : NON-LOCAL POTENTIAL Time : 0.122797146207 (SEC) + + start_pot = atomic + DONE : INIT POTENTIAL Time : 0.135785 (SEC) + + + Make real space PAO into reciprocal space. + max mesh points in Pseudopotential = 601 + dq(describe PAO in reciprocal space) = 0.01 + max q = 542 + + number of pseudo atomic orbitals for Si is 0 + DONE : INIT BASIS Time : 0.184089 (SEC) + + ...............Nose-Hoover Chain parameter initialization............... + Temperature = 3.16682e-05 + Temperature2 = 10.0004 + NHC frequency = 0.00120944 + NHC chain = 4 + Qmass = 1823.61 + ............................................................... + + PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + K-point CG iter num Time(Sec) + 1 6.125000 0.314119 + 2 6.500000 0.327905 + 3 6.750000 0.334448 + 4 6.125000 0.309547 + 5 6.750000 0.112520 + 6 6.125000 0.024925 + 7 5.875000 0.024036 + 8 6.250000 0.025291 + + Density error is 0.108050841230 + + PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + K-point CG iter num Time(Sec) + 1 2.500000 0.012342 + 2 2.250000 0.011339 + 3 2.625000 0.012621 + 4 3.250000 0.014770 + 5 2.500000 0.012183 + 6 3.125000 0.014333 + 7 2.125000 0.010831 + 8 2.625000 0.012575 + + Density error is 0.004334778560 + + PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + K-point CG iter num Time(Sec) + 1 3.375000 0.015399 + 2 3.250000 0.014874 + 3 3.125000 0.014380 + 4 4.000000 0.017413 + 5 3.250000 0.014776 + 6 4.000000 0.017425 + 7 3.750000 0.016523 + 8 2.875000 0.013438 + + Density error is 0.000134739187 + + PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + K-point CG iter num Time(Sec) + 1 3.750000 0.016717 + 2 3.250000 0.014854 + 3 3.375000 0.015229 + 4 4.000000 0.017399 + 5 3.500000 0.015669 + 6 4.000000 0.017380 + 7 4.500000 0.019148 + 8 3.375000 0.015188 + + Density error is 0.000014649703 + + PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + K-point CG iter num Time(Sec) + 1 2.750000 0.013183 + 2 2.625000 0.012728 + 3 2.750000 0.013067 + 4 2.750000 0.013018 + 5 2.875000 0.013453 + 6 2.750000 0.013008 + 7 2.625000 0.012593 + 8 2.625000 0.012567 + + Density error is 0.000000599415 + + PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + K-point CG iter num Time(Sec) + 1 3.125000 0.014489 + 2 3.625000 0.016131 + 3 3.250000 0.014781 + 4 4.375000 0.018739 + 5 3.375000 0.015250 + 6 4.000000 0.017425 + 7 4.250000 0.018253 + 8 3.375000 0.015213 + + Density error is 0.000000048534 + + PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + K-point CG iter num Time(Sec) + 1 3.250000 0.015027 + 2 3.000000 0.013998 + 3 3.125000 0.014375 + 4 3.625000 0.016117 + 5 3.000000 0.013941 + 6 4.125000 0.017842 + 7 3.500000 0.015638 + 8 3.125000 0.014323 + + Density error is 0.000000002823 + + PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + K-point CG iter num Time(Sec) + 1 3.500000 0.015909 + 2 3.125000 0.014437 + 3 3.000000 0.013954 + 4 3.500000 0.015692 + 5 3.250000 0.014873 + 6 3.250000 0.014791 + 7 3.375000 0.015237 + 8 3.125000 0.014335 + + Density error is 0.000000000061 + + charge density convergence is achieved + final etot is -211.771832657158 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.885363 +0.500467 +0.150240 + Si2 +0.885363 -0.500467 -0.150240 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.045273 -3.807537 -13.541448 + -3.807537 +124.421298 +24.047975 + -13.541448 +24.047975 +125.016023 + +output Pressure for check! +Virtual Pressure is +124.231102 Kbar +Virial is +124.160865 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 1 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564005 (Rydberg) + NVT Temperature : +10.000364 (K) + NVT Kinetic energy : +0.000190 (Rydberg) + NVT Potential energy : -15.564937 (Rydberg) + maxForce : +0.000400 + maxStep : +0.012800 + MD_STEP SystemE Conserved DeltaE Temperature + +1 -7.782469 -7.782003 +0.000000 +14.311776 + + PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.500000 +1.482434 + +2 +24.125000 +0.314735 + +3 +24.250000 +0.087904 + +4 +27.625000 +0.099392 + +5 +25.000000 +0.090634 + +6 +29.875000 +0.107431 + +7 +31.875000 +0.113921 + +8 +26.750000 +0.096067 + + Density error is +0.000008438536 + + PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010623 + +2 +2.000000 +0.010501 + +3 +2.000000 +0.010437 + +4 +2.000000 +0.010430 + +5 +2.000000 +0.010417 + +6 +2.000000 +0.010392 + +7 +2.000000 +0.010413 + +8 +2.000000 +0.010431 + + Density error is +0.000000589537 + + PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.375000 +0.011909 + +2 +2.125000 +0.010960 + +3 +2.125000 +0.010853 + +4 +2.750000 +0.013046 + +5 +2.000000 +0.010421 + +6 +2.750000 +0.013030 + +7 +3.375000 +0.015237 + +8 +2.125000 +0.010850 + + Density error is +0.000000029687 + + PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.375000 +0.015446 + +2 +3.500000 +0.015794 + +3 +3.125000 +0.014440 + +4 +3.500000 +0.015678 + +5 +3.625000 +0.016125 + +6 +3.500000 +0.015643 + +7 +3.250000 +0.014765 + +8 +3.500000 +0.015638 + + Density error is +0.000000000296 + + charge density convergence is achieved + final etot is -211.778481425683 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.815731 +0.355757 +0.109618 + Si2 +0.815731 -0.355757 -0.109618 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.843178 -2.800524 -9.609977 + -2.800524 +124.232437 +22.152784 + -9.609977 +22.152784 +124.529670 + +output Pressure for check! +Virtual Pressure is +123.968947 Kbar +Virial is +123.868428 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 2 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564050 (Rydberg) + NVT Temperature : +33.255982 (K) + NVT Kinetic energy : +0.000632 (Rydberg) + NVT Potential energy : -15.565426 (Rydberg) + maxForce : +0.000304 + maxStep : +0.026509 + MD_STEP SystemE Conserved DeltaE Temperature + +2 -7.782713 -7.782025 +0.000000 +66.542608 + + PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +33.625000 +1.455297 + +2 +23.000000 +0.344287 + +3 +23.250000 +0.084591 + +4 +27.250000 +0.097961 + +5 +24.625000 +0.089419 + +6 +28.375000 +0.101985 + +7 +26.625000 +0.096635 + +8 +24.625000 +0.089249 + + Density error is +0.000021869323 + + PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010696 + +2 +2.000000 +0.010427 + +3 +2.000000 +0.010429 + +4 +2.000000 +0.010408 + +5 +2.000000 +0.010427 + +6 +2.375000 +0.011750 + +7 +2.000000 +0.010404 + +8 +2.000000 +0.010397 + + Density error is +0.000001763699 + + PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011012 + +2 +2.250000 +0.011394 + +3 +2.250000 +0.011290 + +4 +2.875000 +0.013481 + +5 +2.250000 +0.011358 + +6 +3.000000 +0.013927 + +7 +2.875000 +0.013486 + +8 +2.375000 +0.011717 + + Density error is +0.000000036065 + + PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016348 + +2 +3.750000 +0.016579 + +3 +3.750000 +0.016547 + +4 +4.375000 +0.018704 + +5 +3.500000 +0.015695 + +6 +4.125000 +0.017849 + +7 +4.625000 +0.019620 + +8 +3.625000 +0.016087 + + Density error is +0.000000002244 + + PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013691 + +2 +3.000000 +0.013966 + +3 +2.875000 +0.013492 + +4 +3.875000 +0.016984 + +5 +3.250000 +0.014831 + +6 +3.750000 +0.016559 + +7 +3.000000 +0.013909 + +8 +3.000000 +0.013880 + + Density error is +0.000000000184 + + charge density convergence is achieved + final etot is -211.794269556733 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.462515 +0.083202 +0.018773 + Si2 +0.462515 -0.083202 -0.018773 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.815311 -0.492388 -2.246119 + -0.492388 +123.347654 +12.547878 + -2.246119 +12.547878 +123.364301 + +output Pressure for check! +Virtual Pressure is +123.643118 Kbar +Virial is +123.175755 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 3 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564151 (Rydberg) + NVT Temperature : +88.343003 (K) + NVT Kinetic energy : +0.001679 (Rydberg) + NVT Potential energy : -15.566586 (Rydberg) + maxForce : +0.000084 + maxStep : +0.033756 + MD_STEP SystemE Conserved DeltaE Temperature + +3 -7.783293 -7.782076 +0.000000 +112.977290 + + PW ALGORITHM --------------- ION=+4 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +37.125000 +1.584397 + +2 +24.625000 +0.212187 + +3 +25.750000 +0.092986 + +4 +29.250000 +0.104765 + +5 +27.000000 +0.097458 + +6 +31.875000 +0.113833 + +7 +28.250000 +0.101426 + +8 +25.250000 +0.091166 + + Density error is +0.000033429323 + + PW ALGORITHM --------------- ION=+4 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010606 + +2 +2.000000 +0.010470 + +3 +2.000000 +0.010394 + +4 +2.000000 +0.010391 + +5 +2.000000 +0.010403 + +6 +2.000000 +0.010374 + +7 +2.000000 +0.010374 + +8 +2.000000 +0.010432 + + Density error is +0.000002801781 + + PW ALGORITHM --------------- ION=+4 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011027 + +2 +2.500000 +0.012197 + +3 +2.250000 +0.011338 + +4 +2.375000 +0.011707 + +5 +2.250000 +0.011301 + +6 +2.625000 +0.012578 + +7 +2.875000 +0.013474 + +8 +2.375000 +0.011758 + + Density error is +0.000000035628 + + PW ALGORITHM --------------- ION=+4 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.875000 +0.017185 + +2 +3.875000 +0.017012 + +3 +3.750000 +0.016533 + +4 +4.000000 +0.017359 + +5 +3.750000 +0.016991 + +6 +3.875000 +0.017340 + +7 +4.625000 +0.019603 + +8 +3.750000 +0.016469 + + Density error is +0.000000003655 + + PW ALGORITHM --------------- ION=+4 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013239 + +2 +2.625000 +0.012645 + +3 +2.750000 +0.013035 + +4 +3.750000 +0.016496 + +5 +2.750000 +0.013016 + +6 +3.250000 +0.014762 + +7 +3.000000 +0.013915 + +8 +2.625000 +0.012541 + + Density error is +0.000000000196 + + charge density convergence is achieved + final etot is -211.798998994521 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.045801 -0.211053 -0.052135 + Si2 -0.045801 +0.211053 +0.052135 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.007250 +1.421851 +5.725860 + +1.421851 +122.897686 -1.245212 + +5.725860 -1.245212 +123.005310 + +output Pressure for check! +Virtual Pressure is +123.763579 Kbar +Virial is +122.970082 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 4 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564177 (Rydberg) + NVT Temperature : +103.974513 (K) + NVT Kinetic energy : +0.001976 (Rydberg) + NVT Potential energy : -15.566934 (Rydberg) + maxForce : +0.000019 + maxStep : +0.030839 + MD_STEP SystemE Conserved DeltaE Temperature + +4 -7.783467 -7.782089 +0.000000 +94.653093 + + PW ALGORITHM --------------- ION=+5 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.125000 +1.541803 + +2 +24.500000 +0.265063 + +3 +26.125000 +0.094359 + +4 +30.250000 +0.108286 + +5 +25.500000 +0.091682 + +6 +28.875000 +0.104719 + +7 +29.250000 +0.105021 + +8 +25.125000 +0.090821 + + Density error is +0.000028572302 + + PW ALGORITHM --------------- ION=+5 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010595 + +2 +2.000000 +0.010418 + +3 +2.000000 +0.010451 + +4 +2.000000 +0.010412 + +5 +2.000000 +0.010426 + +6 +2.000000 +0.010384 + +7 +2.000000 +0.010373 + +8 +2.000000 +0.010418 + + Density error is +0.000002384066 + + PW ALGORITHM --------------- ION=+5 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011011 + +2 +2.375000 +0.011743 + +3 +2.250000 +0.011317 + +4 +2.625000 +0.012578 + +5 +2.250000 +0.011279 + +6 +2.750000 +0.013007 + +7 +2.875000 +0.013443 + +8 +2.375000 +0.011684 + + Density error is +0.000000035575 + + PW ALGORITHM --------------- ION=+5 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016778 + +2 +3.875000 +0.017042 + +3 +3.750000 +0.016539 + +4 +4.125000 +0.017849 + +5 +3.750000 +0.016577 + +6 +3.625000 +0.016055 + +7 +4.625000 +0.019602 + +8 +3.625000 +0.016048 + + Density error is +0.000000003086 + + PW ALGORITHM --------------- ION=+5 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013198 + +2 +2.625000 +0.012687 + +3 +2.875000 +0.013502 + +4 +3.750000 +0.016536 + +5 +2.750000 +0.013120 + +6 +3.375000 +0.015253 + +7 +2.875000 +0.013430 + +8 +2.875000 +0.013424 + + Density error is +0.000000000189 + + charge density convergence is achieved + final etot is -211.787163106063 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.531795 -0.423861 -0.074943 + Si2 -0.531795 +0.423861 +0.074943 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.156562 +2.191352 +11.539648 + +2.191352 +123.421604 -14.461358 + +11.539648 -14.461358 +123.871961 + +output Pressure for check! +Virtual Pressure is +124.148173 Kbar +Virial is +123.483375 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 5 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564100 (Rydberg) + NVT Temperature : +61.015343 (K) + NVT Kinetic energy : +0.001159 (Rydberg) + NVT Potential energy : -15.566064 (Rydberg) + maxForce : +0.000177 + maxStep : +0.019294 + MD_STEP SystemE Conserved DeltaE Temperature + +5 -7.783032 -7.782050 +0.000000 +35.600513 + + PW ALGORITHM --------------- ION=+6 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.750000 +1.538779 + +2 +23.375000 +0.281560 + +3 +26.625000 +0.096030 + +4 +29.375000 +0.105067 + +5 +25.125000 +0.090691 + +6 +30.000000 +0.107285 + +7 +30.125000 +0.107224 + +8 +23.875000 +0.086308 + + Density error is +0.000013559050 + + PW ALGORITHM --------------- ION=+6 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010587 + +2 +2.000000 +0.010411 + +3 +2.000000 +0.010387 + +4 +2.000000 +0.010385 + +5 +2.000000 +0.010401 + +6 +2.000000 +0.010372 + +7 +2.000000 +0.010373 + +8 +2.000000 +0.010387 + + Density error is +0.000001049378 + + PW ALGORITHM --------------- ION=+6 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.010993 + +2 +2.125000 +0.010884 + +3 +2.125000 +0.010912 + +4 +2.500000 +0.012157 + +5 +2.125000 +0.010852 + +6 +2.750000 +0.013010 + +7 +3.000000 +0.013908 + +8 +2.125000 +0.010824 + + Density error is +0.000000034124 + + PW ALGORITHM --------------- ION=+6 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016280 + +2 +3.625000 +0.016107 + +3 +3.625000 +0.016126 + +4 +3.875000 +0.016930 + +5 +3.625000 +0.016102 + +6 +3.625000 +0.016047 + +7 +4.375000 +0.018675 + +8 +3.625000 +0.016036 + + Density error is +0.000000001047 + + PW ALGORITHM --------------- ION=+6 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.250000 +0.015029 + +2 +3.250000 +0.014818 + +3 +3.125000 +0.014333 + +4 +4.500000 +0.019099 + +5 +3.125000 +0.014369 + +6 +4.250000 +0.018282 + +7 +3.250000 +0.014734 + +8 +3.250000 +0.014725 + + Density error is +0.000000000093 + + charge density convergence is achieved + final etot is -211.773976096239 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.830073 -0.488698 -0.076368 + Si2 -0.830073 +0.488698 +0.076368 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.079115 +2.349387 +13.341463 + +2.349387 +124.240376 -22.607891 + +13.341463 -22.607891 +124.847553 + +output Pressure for check! +Virtual Pressure is +124.305722 Kbar +Virial is +124.055681 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 6 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564017 (Rydberg) + NVT Temperature : +13.869106 (K) + NVT Kinetic energy : +0.000264 (Rydberg) + NVT Potential energy : -15.565095 (Rydberg) + maxForce : +0.000353 + maxStep : +0.009591 + MD_STEP SystemE Conserved DeltaE Temperature + +6 -7.782547 -7.782009 +0.000000 +9.461554 + + PW ALGORITHM --------------- ION=+7 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.250000 +1.548029 + +2 +24.625000 +0.276619 + +3 +27.375000 +0.098665 + +4 +30.375000 +0.108527 + +5 +26.375000 +0.095093 + +6 +30.625000 +0.109686 + +7 +31.000000 +0.110332 + +8 +25.250000 +0.091074 + + Density error is +0.000006867857 + + PW ALGORITHM --------------- ION=+7 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010576 + +2 +2.000000 +0.010440 + +3 +2.000000 +0.010510 + +4 +2.000000 +0.010413 + +5 +2.000000 +0.010403 + +6 +2.125000 +0.010838 + +7 +2.000000 +0.010376 + +8 +2.000000 +0.010387 + + Density error is +0.000000471169 + + PW ALGORITHM --------------- ION=+7 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013211 + +2 +2.000000 +0.010520 + +3 +2.000000 +0.010489 + +4 +2.750000 +0.013013 + +5 +2.125000 +0.010843 + +6 +2.500000 +0.012183 + +7 +3.250000 +0.014821 + +8 +2.000000 +0.010417 + + Density error is +0.000000026949 + + PW ALGORITHM --------------- ION=+7 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.000000 +0.014095 + +2 +3.250000 +0.014863 + +3 +3.000000 +0.013942 + +4 +3.125000 +0.014354 + +5 +3.250000 +0.014813 + +6 +3.250000 +0.014752 + +7 +3.500000 +0.015640 + +8 +3.250000 +0.014764 + + Density error is +0.000000000178 + + charge density convergence is achieved + final etot is -211.775966500996 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.841211 -0.388251 -0.083865 + Si2 -0.841211 +0.388251 +0.083865 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.888185 +2.498229 +10.607911 + +2.498229 +124.324706 -22.903208 + +10.607911 -22.903208 +124.699212 + +output Pressure for check! +Virtual Pressure is +124.037154 Kbar +Virial is +123.970701 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 7 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564029 (Rydberg) + NVT Temperature : +20.830773 (K) + NVT Kinetic energy : +0.000396 (Rydberg) + NVT Potential energy : -15.565241 (Rydberg) + maxForce : +0.000327 + maxStep : +0.022260 + MD_STEP SystemE Conserved DeltaE Temperature + +7 -7.782620 -7.782015 +0.000000 +47.763680 + + PW ALGORITHM --------------- ION=+8 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.625000 +1.498024 + +2 +22.500000 +0.296778 + +3 +24.500000 +0.088638 + +4 +28.750000 +0.103008 + +5 +24.000000 +0.086877 + +6 +29.375000 +0.105138 + +7 +26.250000 +0.094433 + +8 +22.375000 +0.081172 + + Density error is +0.000016498376 + + PW ALGORITHM --------------- ION=+8 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010574 + +2 +2.000000 +0.010443 + +3 +2.000000 +0.010379 + +4 +2.000000 +0.010399 + +5 +2.000000 +0.010420 + +6 +2.000000 +0.010425 + +7 +2.500000 +0.012164 + +8 +2.000000 +0.010416 + + Density error is +0.000001314992 + + PW ALGORITHM --------------- ION=+8 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011051 + +2 +2.250000 +0.011345 + +3 +2.125000 +0.010869 + +4 +2.750000 +0.013016 + +5 +2.250000 +0.011286 + +6 +2.750000 +0.013011 + +7 +3.125000 +0.014347 + +8 +2.250000 +0.011259 + + Density error is +0.000000033932 + + PW ALGORITHM --------------- ION=+8 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.017140 + +2 +3.625000 +0.016310 + +3 +3.750000 +0.016631 + +4 +4.000000 +0.017495 + +5 +3.500000 +0.015705 + +6 +4.125000 +0.017878 + +7 +4.250000 +0.018300 + +8 +3.500000 +0.015635 + + Density error is +0.000000001483 + + PW ALGORITHM --------------- ION=+8 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013210 + +2 +3.125000 +0.014428 + +3 +3.125000 +0.014340 + +4 +4.000000 +0.017385 + +5 +3.125000 +0.014518 + +6 +3.625000 +0.016115 + +7 +3.500000 +0.015627 + +8 +3.375000 +0.015173 + + Density error is +0.000000000115 + + charge density convergence is achieved + final etot is -211.790638622284 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.562521 -0.158433 -0.082597 + Si2 -0.562521 +0.158433 +0.082597 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.818911 +2.300863 +4.331819 + +2.300863 +123.569280 -15.284717 + +4.331819 -15.284717 +123.616732 + +output Pressure for check! +Virtual Pressure is +123.670443 Kbar +Virial is +123.334974 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 8 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564121 (Rydberg) + NVT Temperature : +72.197413 (K) + NVT Kinetic energy : +0.001372 (Rydberg) + NVT Potential energy : -15.566319 (Rydberg) + maxForce : +0.000132 + maxStep : +0.031989 + MD_STEP SystemE Conserved DeltaE Temperature + +8 -7.783160 -7.782060 +0.000000 +101.706395 + + PW ALGORITHM --------------- ION=+9 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.875000 +1.531937 + +2 +26.875000 +0.264962 + +3 +26.750000 +0.096733 + +4 +30.375000 +0.108739 + +5 +27.000000 +0.097620 + +6 +31.875000 +0.114026 + +7 +28.000000 +0.100499 + +8 +25.250000 +0.092090 + + Density error is +0.000030268617 + + PW ALGORITHM --------------- ION=+9 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010942 + +2 +2.000000 +0.010442 + +3 +2.000000 +0.010413 + +4 +2.000000 +0.010444 + +5 +2.000000 +0.010413 + +6 +2.000000 +0.010372 + +7 +2.000000 +0.010379 + +8 +2.000000 +0.010382 + + Density error is +0.000002526424 + + PW ALGORITHM --------------- ION=+9 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011021 + +2 +2.500000 +0.012194 + +3 +2.250000 +0.011346 + +4 +2.375000 +0.011731 + +5 +2.250000 +0.011785 + +6 +2.750000 +0.013400 + +7 +2.875000 +0.013483 + +8 +2.500000 +0.012132 + + Density error is +0.000000035287 + + PW ALGORITHM --------------- ION=+9 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016272 + +2 +3.750000 +0.016595 + +3 +3.625000 +0.016152 + +4 +3.875000 +0.016950 + +5 +3.625000 +0.016113 + +6 +3.750000 +0.016497 + +7 +4.625000 +0.019580 + +8 +3.750000 +0.016488 + + Density error is +0.000000003280 + + PW ALGORITHM --------------- ION=+9 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013195 + +2 +2.750000 +0.013069 + +3 +2.875000 +0.013452 + +4 +4.250000 +0.018388 + +5 +2.875000 +0.013480 + +6 +3.500000 +0.015655 + +7 +3.000000 +0.013869 + +8 +2.625000 +0.012553 + + Density error is +0.000000000193 + + charge density convergence is achieved + final etot is -211.799689533651 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.088600 +0.125590 -0.036123 + Si2 -0.088600 -0.125590 +0.036123 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.942319 +0.972401 -3.404364 + +0.972401 +122.922036 -2.403271 + -3.404364 -2.403271 +122.959321 + +output Pressure for check! +Virtual Pressure is +123.655562 Kbar +Virial is +122.941225 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 9 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564178 (Rydberg) + NVT Temperature : +102.774866 (K) + NVT Kinetic energy : +0.001953 (Rydberg) + NVT Potential energy : -15.566984 (Rydberg) + maxForce : +0.000009 + maxStep : +0.032288 + MD_STEP SystemE Conserved DeltaE Temperature + +9 -7.783492 -7.782089 +0.000000 +102.692994 + + PW ALGORITHM --------------- ION=+10 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.000000 +1.538429 + +2 +24.875000 +0.260502 + +3 +25.750000 +0.093167 + +4 +29.875000 +0.106972 + +5 +26.000000 +0.094130 + +6 +30.000000 +0.107537 + +7 +31.000000 +0.110836 + +8 +25.375000 +0.091698 + + Density error is +0.000030737201 + + PW ALGORITHM --------------- ION=+10 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010666 + +2 +2.000000 +0.010444 + +3 +2.000000 +0.010477 + +4 +2.000000 +0.010404 + +5 +2.000000 +0.010414 + +6 +2.000000 +0.010377 + +7 +2.000000 +0.010374 + +8 +2.000000 +0.010388 + + Density error is +0.000002560646 + + PW ALGORITHM --------------- ION=+10 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.250000 +0.011451 + +2 +2.500000 +0.012257 + +3 +2.250000 +0.011301 + +4 +2.750000 +0.013040 + +5 +2.250000 +0.011288 + +6 +2.625000 +0.012593 + +7 +3.000000 +0.013923 + +8 +2.500000 +0.012151 + + Density error is +0.000000033975 + + PW ALGORITHM --------------- ION=+10 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016339 + +2 +3.875000 +0.017015 + +3 +3.750000 +0.016527 + +4 +4.250000 +0.018269 + +5 +3.750000 +0.016535 + +6 +3.750000 +0.016493 + +7 +4.625000 +0.019590 + +8 +3.750000 +0.016482 + + Density error is +0.000000003387 + + PW ALGORITHM --------------- ION=+10 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013682 + +2 +2.625000 +0.012626 + +3 +2.750000 +0.013042 + +4 +3.750000 +0.016591 + +5 +3.000000 +0.013926 + +6 +3.500000 +0.015660 + +7 +3.000000 +0.013942 + +8 +2.625000 +0.012582 + + Density error is +0.000000000211 + + charge density convergence is achieved + final etot is -211.791757080168 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.416931 +0.372190 +0.054656 + Si2 +0.416931 -0.372190 -0.054656 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.112004 -1.386177 -10.090684 + -1.386177 +123.202765 +11.305489 + -10.090684 +11.305489 +123.552704 + +output Pressure for check! +Virtual Pressure is +124.010423 Kbar +Virial is +123.289157 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 10 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564126 (Rydberg) + NVT Temperature : +73.190993 (K) + NVT Kinetic energy : +0.001391 (Rydberg) + NVT Potential energy : -15.566401 (Rydberg) + maxForce : +0.000119 + maxStep : +0.022835 + MD_STEP SystemE Conserved DeltaE Temperature + +10 -7.783201 -7.782063 +0.000000 +48.734190 + + PW ALGORITHM --------------- ION=+11 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.875000 +1.541778 + +2 +25.500000 +0.266144 + +3 +25.250000 +0.091185 + +4 +29.250000 +0.104785 + +5 +24.875000 +0.090153 + +6 +30.625000 +0.109517 + +7 +28.875000 +0.103393 + +8 +27.500000 +0.098937 + + Density error is +0.000016935127 + + PW ALGORITHM --------------- ION=+11 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010679 + +2 +2.000000 +0.010521 + +3 +2.000000 +0.010402 + +4 +2.000000 +0.010379 + +5 +2.000000 +0.010446 + +6 +2.000000 +0.010416 + +7 +2.000000 +0.010382 + +8 +2.000000 +0.010370 + + Density error is +0.000001343508 + + PW ALGORITHM --------------- ION=+11 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.010997 + +2 +2.125000 +0.010874 + +3 +2.250000 +0.011252 + +4 +2.625000 +0.012581 + +5 +2.125000 +0.010886 + +6 +2.625000 +0.012585 + +7 +3.000000 +0.013888 + +8 +2.375000 +0.011709 + + Density error is +0.000000032255 + + PW ALGORITHM --------------- ION=+11 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016894 + +2 +3.750000 +0.016617 + +3 +3.625000 +0.016129 + +4 +3.875000 +0.016962 + +5 +3.750000 +0.016549 + +6 +3.750000 +0.016487 + +7 +4.500000 +0.019118 + +8 +3.500000 +0.015592 + + Density error is +0.000000001579 + + PW ALGORITHM --------------- ION=+11 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013663 + +2 +3.125000 +0.014367 + +3 +2.875000 +0.013494 + +4 +4.125000 +0.017819 + +5 +3.125000 +0.014308 + +6 +4.000000 +0.017389 + +7 +3.125000 +0.014286 + +8 +3.125000 +0.014297 + + Density error is +0.000000000113 + + charge density convergence is achieved + final etot is -211.777136772291 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.774114 +0.493555 +0.132287 + Si2 +0.774114 -0.493555 -0.132287 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.125513 -3.354234 -13.360634 + -3.354234 +124.042603 +21.012997 + -13.360634 +21.012997 +124.630461 + +output Pressure for check! +Virtual Pressure is +124.275144 Kbar +Virial is +123.932859 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 11 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564029 (Rydberg) + NVT Temperature : +20.916618 (K) + NVT Kinetic energy : +0.000397 (Rydberg) + NVT Potential energy : -15.565327 (Rydberg) + maxForce : +0.000325 + maxStep : +0.009427 + MD_STEP SystemE Conserved DeltaE Temperature + +11 -7.782663 -7.782015 +0.000000 +9.036895 + + PW ALGORITHM --------------- ION=+12 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.125000 +1.547415 + +2 +26.375000 +0.264168 + +3 +25.375000 +0.091673 + +4 +29.500000 +0.105644 + +5 +26.125000 +0.094314 + +6 +31.500000 +0.112479 + +7 +29.875000 +0.106803 + +8 +28.625000 +0.102367 + + Density error is +0.000006530970 + + PW ALGORITHM --------------- ION=+12 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010577 + +2 +2.000000 +0.010466 + +3 +2.000000 +0.010402 + +4 +2.000000 +0.010371 + +5 +2.000000 +0.010404 + +6 +2.000000 +0.010385 + +7 +2.000000 +0.010377 + +8 +2.000000 +0.010356 + + Density error is +0.000000440898 + + PW ALGORITHM --------------- ION=+12 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.625000 +0.012786 + +2 +2.000000 +0.010477 + +3 +2.000000 +0.010393 + +4 +2.750000 +0.013027 + +5 +2.125000 +0.010923 + +6 +2.750000 +0.012995 + +7 +3.125000 +0.014337 + +8 +2.000000 +0.010365 + + Density error is +0.000000024207 + + PW ALGORITHM --------------- ION=+12 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.000000 +0.014107 + +2 +3.125000 +0.014392 + +3 +3.000000 +0.013912 + +4 +3.375000 +0.015251 + +5 +3.375000 +0.015234 + +6 +3.125000 +0.014438 + +7 +3.250000 +0.014784 + +8 +3.250000 +0.014731 + + Density error is +0.000000000170 + + charge density convergence is achieved + final etot is -211.774943325509 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.854779 +0.436696 +0.135045 + Si2 +0.854779 -0.436696 -0.135045 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.950297 -3.436598 -11.810037 + -3.436598 +124.343261 +23.217684 + -11.810037 +23.217684 +124.792605 + +output Pressure for check! +Virtual Pressure is +124.092191 Kbar +Virial is +124.028721 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 12 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564015 (Rydberg) + NVT Temperature : +13.061843 (K) + NVT Kinetic energy : +0.000248 (Rydberg) + NVT Potential energy : -15.565166 (Rydberg) + maxForce : +0.000355 + maxStep : +0.019395 + MD_STEP SystemE Conserved DeltaE Temperature + +12 -7.782583 -7.782007 +0.000000 +34.185920 + + PW ALGORITHM --------------- ION=+13 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.000000 +1.465002 + +2 +23.000000 +0.338683 + +3 +23.500000 +0.085138 + +4 +27.875000 +0.099984 + +5 +24.000000 +0.086926 + +6 +28.875000 +0.103425 + +7 +30.250000 +0.108009 + +8 +24.000000 +0.086816 + + Density error is +0.000013073792 + + PW ALGORITHM --------------- ION=+13 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010625 + +2 +2.000000 +0.010427 + +3 +2.000000 +0.010396 + +4 +2.000000 +0.010386 + +5 +2.000000 +0.010431 + +6 +2.000000 +0.010378 + +7 +2.000000 +0.010379 + +8 +2.000000 +0.010393 + + Density error is +0.000001008013 + + PW ALGORITHM --------------- ION=+13 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011016 + +2 +2.250000 +0.011351 + +3 +2.125000 +0.010831 + +4 +2.750000 +0.013017 + +5 +2.125000 +0.010830 + +6 +2.750000 +0.013067 + +7 +3.125000 +0.014333 + +8 +2.250000 +0.011270 + + Density error is +0.000000030793 + + PW ALGORITHM --------------- ION=+13 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016352 + +2 +3.500000 +0.015679 + +3 +3.625000 +0.016117 + +4 +3.875000 +0.016947 + +5 +3.625000 +0.016079 + +6 +3.750000 +0.016476 + +7 +4.250000 +0.018229 + +8 +3.500000 +0.015618 + + Density error is +0.000000001065 + + PW ALGORITHM --------------- ION=+13 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013652 + +2 +3.375000 +0.015279 + +3 +3.125000 +0.014327 + +4 +4.125000 +0.017830 + +5 +3.250000 +0.014748 + +6 +4.250000 +0.018231 + +7 +3.500000 +0.015621 + +8 +3.375000 +0.015172 + + Density error is +0.000000000097 + + charge density convergence is achieved + final etot is -211.787892336077 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.634765 +0.219902 +0.063772 + Si2 +0.634765 -0.219902 -0.063772 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.810989 -1.646977 -5.949715 + -1.646977 +123.724465 +17.235456 + -5.949715 +17.235456 +123.839274 + +output Pressure for check! +Virtual Pressure is +123.698348 Kbar +Virial is +123.458243 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 13 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564100 (Rydberg) + NVT Temperature : +58.268396 (K) + NVT Kinetic energy : +0.001107 (Rydberg) + NVT Potential energy : -15.566117 (Rydberg) + maxForce : +0.000172 + maxStep : +0.030214 + MD_STEP SystemE Conserved DeltaE Temperature + +13 -7.783059 -7.782050 +0.000000 +89.458675 + + PW ALGORITHM --------------- ION=+14 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.875000 +1.542133 + +2 +26.125000 +0.252769 + +3 +27.000000 +0.097434 + +4 +31.125000 +0.111257 + +5 +27.250000 +0.098368 + +6 +30.375000 +0.108770 + +7 +28.125000 +0.101032 + +8 +27.000000 +0.097412 + + Density error is +0.000027152014 + + PW ALGORITHM --------------- ION=+14 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010571 + +2 +2.000000 +0.010418 + +3 +2.000000 +0.010469 + +4 +2.000000 +0.010378 + +5 +2.000000 +0.010391 + +6 +2.125000 +0.010816 + +7 +2.000000 +0.010413 + +8 +2.000000 +0.010387 + + Density error is +0.000002253887 + + PW ALGORITHM --------------- ION=+14 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011042 + +2 +2.375000 +0.011756 + +3 +2.250000 +0.011280 + +4 +2.750000 +0.013020 + +5 +2.250000 +0.011259 + +6 +2.625000 +0.012556 + +7 +2.875000 +0.013452 + +8 +2.500000 +0.012282 + + Density error is +0.000000033052 + + PW ALGORITHM --------------- ION=+14 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.875000 +0.017209 + +2 +3.750000 +0.016568 + +3 +3.625000 +0.016133 + +4 +4.250000 +0.018248 + +5 +3.625000 +0.016119 + +6 +4.250000 +0.018240 + +7 +4.750000 +0.020036 + +8 +3.625000 +0.016022 + + Density error is +0.000000002963 + + PW ALGORITHM --------------- ION=+14 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013700 + +2 +2.750000 +0.013049 + +3 +2.750000 +0.012990 + +4 +3.500000 +0.015607 + +5 +3.000000 +0.013859 + +6 +3.375000 +0.015179 + +7 +2.875000 +0.013422 + +8 +2.750000 +0.012955 + + Density error is +0.000000000187 + + charge density convergence is achieved + final etot is -211.799136169946 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.198870 -0.070672 -0.020734 + Si2 +0.198870 +0.070672 +0.020734 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.902575 +0.551658 +1.913429 + +0.551658 +122.991496 +5.397063 + +1.913429 +5.397063 +123.003398 + +output Pressure for check! +Virtual Pressure is +123.594137 Kbar +Virial is +122.965823 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 14 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564168 (Rydberg) + NVT Temperature : +96.770497 (K) + NVT Kinetic energy : +0.001839 (Rydberg) + NVT Potential energy : -15.566944 (Rydberg) + maxForce : +0.000017 + maxStep : +0.032116 + MD_STEP SystemE Conserved DeltaE Temperature + +14 -7.783472 -7.782084 +0.000000 +103.109630 + + PW ALGORITHM --------------- ION=+15 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.375000 +1.505918 + +2 +24.375000 +0.254664 + +3 +24.625000 +0.089084 + +4 +30.625000 +0.109605 + +5 +26.625000 +0.095625 + +6 +29.125000 +0.104515 + +7 +27.875000 +0.100128 + +8 +24.500000 +0.088547 + + Density error is +0.000030393373 + + PW ALGORITHM --------------- ION=+15 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010563 + +2 +2.000000 +0.010432 + +3 +2.000000 +0.010404 + +4 +2.000000 +0.010375 + +5 +2.000000 +0.010381 + +6 +2.000000 +0.010377 + +7 +2.000000 +0.010377 + +8 +2.000000 +0.010354 + + Density error is +0.000002547296 + + PW ALGORITHM --------------- ION=+15 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.250000 +0.011476 + +2 +2.500000 +0.012193 + +3 +2.250000 +0.011277 + +4 +2.750000 +0.013015 + +5 +2.250000 +0.011319 + +6 +2.750000 +0.013017 + +7 +2.750000 +0.013009 + +8 +2.500000 +0.012125 + + Density error is +0.000000032257 + + PW ALGORITHM --------------- ION=+15 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016335 + +2 +3.875000 +0.016993 + +3 +3.750000 +0.016491 + +4 +4.375000 +0.018723 + +5 +3.750000 +0.016532 + +6 +3.500000 +0.015608 + +7 +4.375000 +0.018691 + +8 +3.750000 +0.016462 + + Density error is +0.000000003366 + + PW ALGORITHM --------------- ION=+15 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013287 + +2 +2.625000 +0.012630 + +3 +2.875000 +0.013438 + +4 +3.500000 +0.015728 + +5 +2.750000 +0.013063 + +6 +3.125000 +0.014314 + +7 +3.250000 +0.014752 + +8 +2.625000 +0.012547 + + Density error is +0.000000000185 + + charge density convergence is achieved + final etot is -211.794739884606 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.297987 -0.327806 -0.066082 + Si2 -0.297987 +0.327806 +0.066082 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.100328 +1.856002 +8.909136 + +1.856002 +123.052207 -8.099784 + +8.909136 -8.099784 +123.317967 + +output Pressure for check! +Virtual Pressure is +123.881026 Kbar +Virial is +123.156834 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 15 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564136 (Rydberg) + NVT Temperature : +79.642870 (K) + NVT Kinetic energy : +0.001513 (Rydberg) + NVT Potential energy : -15.566621 (Rydberg) + maxForce : +0.000076 + maxStep : +0.024468 + MD_STEP SystemE Conserved DeltaE Temperature + +15 -7.783310 -7.782068 +0.000000 +58.786721 + + PW ALGORITHM --------------- ION=+16 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.000000 +1.550421 + +2 +24.125000 +0.253604 + +3 +26.125000 +0.094431 + +4 +29.625000 +0.106054 + +5 +25.500000 +0.091700 + +6 +29.500000 +0.105684 + +7 +29.125000 +0.104354 + +8 +23.750000 +0.086118 + + Density error is +0.000019003017 + + PW ALGORITHM --------------- ION=+16 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010587 + +2 +2.000000 +0.010446 + +3 +2.000000 +0.010445 + +4 +2.000000 +0.010404 + +5 +2.000000 +0.010390 + +6 +2.000000 +0.010379 + +7 +2.000000 +0.010378 + +8 +2.000000 +0.010370 + + Density error is +0.000001546864 + + PW ALGORITHM --------------- ION=+16 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011046 + +2 +2.375000 +0.011756 + +3 +2.250000 +0.011289 + +4 +2.500000 +0.012140 + +5 +2.250000 +0.011313 + +6 +2.750000 +0.013017 + +7 +2.875000 +0.013462 + +8 +2.250000 +0.011249 + + Density error is +0.000000031769 + + PW ALGORITHM --------------- ION=+16 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016761 + +2 +3.500000 +0.015694 + +3 +3.750000 +0.016521 + +4 +4.000000 +0.017360 + +5 +3.500000 +0.015655 + +6 +3.625000 +0.016032 + +7 +4.625000 +0.019569 + +8 +3.625000 +0.016039 + + Density error is +0.000000001918 + + PW ALGORITHM --------------- ION=+16 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013196 + +2 +3.125000 +0.014455 + +3 +2.875000 +0.013481 + +4 +4.000000 +0.017394 + +5 +3.000000 +0.013924 + +6 +3.750000 +0.016493 + +7 +3.000000 +0.013924 + +8 +3.125000 +0.014310 + + Density error is +0.000000000142 + + charge density convergence is achieved + final etot is -211.780796729120 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.685454 -0.466777 -0.074732 + Si2 -0.685454 +0.466777 +0.074732 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.145046 +2.237882 +12.724721 + +2.237882 +123.794533 -18.656690 + +12.724721 -18.656690 +124.345426 + +output Pressure for check! +Virtual Pressure is +124.174558 Kbar +Virial is +123.761668 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 16 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564047 (Rydberg) + NVT Temperature : +29.284447 (K) + NVT Kinetic energy : +0.000556 (Rydberg) + NVT Potential energy : -15.565596 (Rydberg) + maxForce : +0.000262 + maxStep : +0.011494 + MD_STEP SystemE Conserved DeltaE Temperature + +16 -7.782798 -7.782023 +0.000000 +12.500370 + + PW ALGORITHM --------------- ION=+17 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.250000 +1.548769 + +2 +24.250000 +0.238733 + +3 +26.875000 +0.097094 + +4 +30.500000 +0.109091 + +5 +25.500000 +0.092283 + +6 +29.500000 +0.106987 + +7 +30.375000 +0.108359 + +8 +24.000000 +0.086977 + + Density error is +0.000007183223 + + PW ALGORITHM --------------- ION=+17 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010577 + +2 +2.000000 +0.010427 + +3 +2.000000 +0.010496 + +4 +2.000000 +0.010394 + +5 +2.000000 +0.010418 + +6 +2.125000 +0.010931 + +7 +2.000000 +0.010379 + +8 +2.000000 +0.010422 + + Density error is +0.000000511477 + + PW ALGORITHM --------------- ION=+17 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.375000 +0.011921 + +2 +2.125000 +0.010910 + +3 +2.125000 +0.010844 + +4 +2.875000 +0.013531 + +5 +2.000000 +0.010405 + +6 +2.625000 +0.012594 + +7 +3.375000 +0.015197 + +8 +2.125000 +0.010844 + + Density error is +0.000000026283 + + PW ALGORITHM --------------- ION=+17 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.375000 +0.015456 + +2 +3.625000 +0.016132 + +3 +3.250000 +0.014828 + +4 +3.500000 +0.015635 + +5 +3.375000 +0.015239 + +6 +3.375000 +0.015161 + +7 +3.125000 +0.014336 + +8 +3.500000 +0.015643 + + Density error is +0.000000000237 + + charge density convergence is achieved + final etot is -211.774985509926 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.833310 -0.445812 -0.078719 + Si2 -0.833310 +0.445812 +0.078719 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.994195 +2.379118 +12.171980 + +2.379118 +124.272817 -22.694125 + +12.171980 -22.694125 +124.774373 + +output Pressure for check! +Virtual Pressure is +124.101591 Kbar +Virial is +124.013795 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 17 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564010 (Rydberg) + NVT Temperature : +8.524394 (K) + NVT Kinetic energy : +0.000162 (Rydberg) + NVT Potential energy : -15.565169 (Rydberg) + maxForce : +0.000340 + maxStep : +0.014988 + MD_STEP SystemE Conserved DeltaE Temperature + +17 -7.782584 -7.782005 +0.000000 +21.039416 + + PW ALGORITHM --------------- ION=+18 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.250000 +1.473409 + +2 +22.000000 +0.326542 + +3 +24.000000 +0.087028 + +4 +28.000000 +0.100599 + +5 +24.000000 +0.086910 + +6 +29.000000 +0.103884 + +7 +27.125000 +0.097431 + +8 +21.625000 +0.078627 + + Density error is +0.000009301236 + + PW ALGORITHM --------------- ION=+18 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010625 + +2 +2.000000 +0.010448 + +3 +2.000000 +0.010394 + +4 +2.000000 +0.010369 + +5 +2.000000 +0.010395 + +6 +2.125000 +0.010809 + +7 +2.000000 +0.010374 + +8 +2.000000 +0.010352 + + Density error is +0.000000698839 + + PW ALGORITHM --------------- ION=+18 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.250000 +0.011468 + +2 +2.125000 +0.010873 + +3 +2.125000 +0.010841 + +4 +2.875000 +0.013464 + +5 +2.125000 +0.010821 + +6 +2.500000 +0.012141 + +7 +3.125000 +0.014320 + +8 +2.125000 +0.010803 + + Density error is +0.000000028756 + + PW ALGORITHM --------------- ION=+18 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.500000 +0.015856 + +2 +3.625000 +0.016113 + +3 +3.500000 +0.015631 + +4 +3.625000 +0.016042 + +5 +3.625000 +0.016071 + +6 +3.750000 +0.016468 + +7 +4.000000 +0.017389 + +8 +3.625000 +0.016045 + + Density error is +0.000000000545 + + charge density convergence is achieved + final etot is -211.784530531570 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.693682 -0.275109 -0.084557 + Si2 -0.693682 +0.275109 +0.084557 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.844932 +2.424056 +7.513685 + +2.424056 +123.890142 -18.864028 + +7.513685 -18.864028 +124.067900 + +output Pressure for check! +Virtual Pressure is +123.748762 Kbar +Virial is +123.600991 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 18 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564069 (Rydberg) + NVT Temperature : +42.047874 (K) + NVT Kinetic energy : +0.000799 (Rydberg) + NVT Potential energy : -15.565870 (Rydberg) + maxForce : +0.000213 + maxStep : +0.027051 + MD_STEP SystemE Conserved DeltaE Temperature + +18 -7.782935 -7.782034 +0.000000 +72.297418 + + PW ALGORITHM --------------- ION=+19 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +33.625000 +1.446761 + +2 +22.750000 +0.337746 + +3 +24.500000 +0.088664 + +4 +26.875000 +0.096374 + +5 +24.375000 +0.088118 + +6 +27.625000 +0.099005 + +7 +26.125000 +0.093894 + +8 +23.000000 +0.083275 + + Density error is +0.000022341414 + + PW ALGORITHM --------------- ION=+19 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010590 + +2 +2.000000 +0.010429 + +3 +2.000000 +0.010400 + +4 +2.500000 +0.012143 + +5 +2.000000 +0.010418 + +6 +2.000000 +0.010354 + +7 +2.375000 +0.011685 + +8 +2.000000 +0.010357 + + Density error is +0.000001840522 + + PW ALGORITHM --------------- ION=+19 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011068 + +2 +2.375000 +0.011775 + +3 +2.250000 +0.011276 + +4 +2.500000 +0.012134 + +5 +2.250000 +0.011291 + +6 +2.500000 +0.012133 + +7 +3.000000 +0.013910 + +8 +2.375000 +0.011695 + + Density error is +0.000000031328 + + PW ALGORITHM --------------- ION=+19 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016750 + +2 +3.750000 +0.016541 + +3 +3.750000 +0.016522 + +4 +4.000000 +0.017360 + +5 +3.625000 +0.016071 + +6 +3.875000 +0.016922 + +7 +4.125000 +0.017815 + +8 +3.875000 +0.016914 + + Density error is +0.000000002386 + + PW ALGORITHM --------------- ION=+19 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013224 + +2 +2.875000 +0.013511 + +3 +2.875000 +0.013467 + +4 +3.875000 +0.016967 + +5 +2.875000 +0.013449 + +6 +3.500000 +0.015602 + +7 +3.500000 +0.015614 + +8 +2.500000 +0.012112 + + Density error is +0.000000000165 + + charge density convergence is achieved + final etot is -211.797509996802 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.315435 -0.012610 -0.062567 + Si2 -0.315435 +0.012610 +0.062567 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.869560 +1.699030 +0.355976 + +1.699030 +123.125358 -8.562365 + +0.355976 -8.562365 +123.115733 + +output Pressure for check! +Virtual Pressure is +123.544666 Kbar +Virial is +123.036884 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 19 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564150 (Rydberg) + NVT Temperature : +86.724314 (K) + NVT Kinetic energy : +0.001648 (Rydberg) + NVT Potential energy : -15.566824 (Rydberg) + maxForce : +0.000039 + maxStep : +0.031849 + MD_STEP SystemE Conserved DeltaE Temperature + +19 -7.783412 -7.782075 +0.000000 +101.072847 + + PW ALGORITHM --------------- ION=+20 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.000000 +1.535621 + +2 +25.500000 +0.274161 + +3 +26.125000 +0.094184 + +4 +29.875000 +0.106798 + +5 +26.375000 +0.095103 + +6 +30.750000 +0.109985 + +7 +31.875000 +0.114172 + +8 +25.750000 +0.092841 + + Density error is +0.000029792721 + + PW ALGORITHM --------------- ION=+20 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011051 + +2 +2.000000 +0.010426 + +3 +2.000000 +0.010378 + +4 +2.125000 +0.010793 + +5 +2.000000 +0.010367 + +6 +2.000000 +0.010355 + +7 +2.000000 +0.010362 + +8 +2.000000 +0.010354 + + Density error is +0.000002500903 + + PW ALGORITHM --------------- ION=+20 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.375000 +0.011932 + +2 +2.500000 +0.012164 + +3 +2.250000 +0.011253 + +4 +2.500000 +0.012117 + +5 +2.250000 +0.011252 + +6 +2.750000 +0.012983 + +7 +2.750000 +0.013005 + +8 +2.500000 +0.012105 + + Density error is +0.000000031164 + + PW ALGORITHM --------------- ION=+20 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016752 + +2 +3.875000 +0.016963 + +3 +3.750000 +0.016481 + +4 +3.875000 +0.016934 + +5 +3.750000 +0.016474 + +6 +3.625000 +0.016019 + +7 +4.750000 +0.019994 + +8 +3.750000 +0.016447 + + Density error is +0.000000003269 + + PW ALGORITHM --------------- ION=+20 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013655 + +2 +2.625000 +0.012594 + +3 +2.625000 +0.012553 + +4 +3.750000 +0.016475 + +5 +2.875000 +0.013402 + +6 +3.500000 +0.015683 + +7 +2.750000 +0.012961 + +8 +2.625000 +0.012526 + + Density error is +0.000000000179 + + charge density convergence is achieved + final etot is -211.797737534802 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.171785 +0.257041 +0.008602 + Si2 +0.171785 -0.257041 -0.008602 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.033300 -0.204765 -6.972062 + -0.204765 +122.939153 +4.657249 + -6.972062 +4.657249 +123.108999 + +output Pressure for check! +Virtual Pressure is +123.737037 Kbar +Virial is +123.027151 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 20 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564150 (Rydberg) + NVT Temperature : +85.566203 (K) + NVT Kinetic energy : +0.001626 (Rydberg) + NVT Potential energy : -15.566841 (Rydberg) + maxForce : +0.000036 + maxStep : +0.026933 + MD_STEP SystemE Conserved DeltaE Temperature + +20 -7.783421 -7.782075 +0.000000 +70.314105 + + PW ALGORITHM --------------- ION=+21 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.125000 +1.533770 + +2 +24.250000 +0.243025 + +3 +24.750000 +0.089487 + +4 +29.750000 +0.106362 + +5 +24.875000 +0.089914 + +6 +29.875000 +0.106912 + +7 +32.125000 +0.114500 + +8 +27.125000 +0.097630 + + Density error is +0.000022029241 + + PW ALGORITHM --------------- ION=+21 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010617 + +2 +2.000000 +0.010405 + +3 +2.000000 +0.010373 + +4 +2.000000 +0.010365 + +5 +2.000000 +0.010388 + +6 +2.000000 +0.010360 + +7 +2.000000 +0.010347 + +8 +2.000000 +0.010369 + + Density error is +0.000001807441 + + PW ALGORITHM --------------- ION=+21 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011063 + +2 +2.375000 +0.011747 + +3 +2.250000 +0.011261 + +4 +2.500000 +0.012112 + +5 +2.250000 +0.011278 + +6 +2.625000 +0.012552 + +7 +3.000000 +0.013891 + +8 +2.375000 +0.011680 + + Density error is +0.000000029382 + + PW ALGORITHM --------------- ION=+21 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016299 + +2 +3.625000 +0.016094 + +3 +3.750000 +0.016491 + +4 +3.875000 +0.016919 + +5 +3.750000 +0.016502 + +6 +3.750000 +0.016462 + +7 +4.625000 +0.019557 + +8 +3.625000 +0.016026 + + Density error is +0.000000002371 + + PW ALGORITHM --------------- ION=+21 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013673 + +2 +2.875000 +0.013455 + +3 +2.875000 +0.013422 + +4 +4.125000 +0.017806 + +5 +3.000000 +0.013879 + +6 +3.875000 +0.016927 + +7 +3.000000 +0.013878 + +8 +2.875000 +0.013406 + + Density error is +0.000000000178 + + charge density convergence is achieved + final etot is -211.785114277951 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.597076 +0.443380 +0.097410 + Si2 +0.597076 -0.443380 -0.097410 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.145634 -2.476538 -12.011339 + -2.476538 +123.557627 +16.195950 + -12.011339 +16.195950 +124.041967 + +output Pressure for check! +Virtual Pressure is +124.075595 Kbar +Virial is +123.581743 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 21 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564066 (Rydberg) + NVT Temperature : +39.619227 (K) + NVT Kinetic energy : +0.000753 (Rydberg) + NVT Potential energy : -15.565913 (Rydberg) + maxForce : +0.000213 + maxStep : +0.014552 + MD_STEP SystemE Conserved DeltaE Temperature + +21 -7.782957 -7.782033 +0.000000 +19.004126 + + + -------------------------------------------- + !FINAL_ETOT_IS -211.7851142779510099 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +35.575 15 +2.37 +100.00 % + Run_pw plane_wave_line +35.54 1 +35.54 +99.91 % + Run_MD_PW md_cells_pw +35.47 1 +35.47 +99.70 % + Potential init_pot +0.21 22 +0.01 +0.59 % + FFT FFT3D +21.26 126906 +0.00 +59.76 % + Potential v_of_rho +1.13 125 +0.01 +3.17 % + H_XC_pw v_xc +1.20 146 +0.01 +3.36 % + wavefunc wfcinit +0.97 22 +0.04 +2.73 % + pp_cell_vnl getvnl +0.46 1336 +0.00 +1.29 % + Hamilt_PW diagH_subspace +3.41 984 +0.00 +9.57 % + Hamilt_PW h_psi +24.29 52236 +0.00 +68.28 % + Hamilt_PW vloc +22.85 52236 +0.00 +64.24 % + Hamilt_PW vnl +1.29 52236 +0.00 +3.63 % + Hamilt_PW add_nonlocal_pp +0.75 52236 +0.00 +2.12 % + Run_MD_PW md_ions_pw +35.39 1 +35.39 +99.48 % + Electrons self_consistent +29.43 21 +1.40 +82.73 % + Electrons c_bands +25.56 103 +0.25 +71.86 % + Hamilt diagH_pw +25.14 824 +0.03 +70.67 % + Diago_CG diag +22.34 824 +0.03 +62.80 % + Charge sum_band +1.54 103 +0.01 +4.32 % + Charge mix_rho +0.20 103 +0.00 +0.57 % + Forces cal_force_nl +0.59 21 +0.03 +1.66 % + Stress_PW cal_stress +3.97 21 +0.19 +11.16 % + Stress_Func stress_ew +16.82 11 +1.53 +47.27 % + Force_Func stress_ew +16.82 11 +1.53 +47.27 % + Stress_Func stress_gga +0.11 21 +0.01 +0.31 % + Stress_Func stres_nl +3.76 21 +0.18 +10.57 % + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +5.1730 + ---------------------------------------------------------- + + Start Time : Fri Oct 15 14:37:16 2021 + Finish Time : Fri Oct 15 14:37:52 2021 + Total Time : 0 h 0 mins 36 secs diff --git a/tests/abacus.md/STRU b/tests/abacus.md/STRU new file mode 100644 index 000000000..c3765e9bc --- /dev/null +++ b/tests/abacus.md/STRU @@ -0,0 +1,21 @@ +ATOMIC_SPECIES +Si 1.000 ./Si_ONCV_PBE-1.0.upf #Element, Mass, Pseudopotential + +NUMERICAL_ORBITAL +./Si_gga_8au_60Ry_2s2p1d.orb + +LATTICE_CONSTANT +10.2 #Lattice constant + +LATTICE_VECTORS +0.5 0.5 0.0 #Lattice vector 1 +0.5 0.0 0.5 #Lattice vector 2 +0.0 0.5 0.5 #Lattice vector 3 + +ATOMIC_POSITIONS +Cartesian #Cartesian(Unit is LATTICE_CONSTANT) +Si #Name of element +0.0 #Magnetic for this element. +2 #Number of atoms +0.00 0.00 0.00 1 1 1 #x,y,z, move_x, move_y, move_z +0.241 0.255 0.251 1 1 1 diff --git a/tests/abacus.md/Si_coord b/tests/abacus.md/Si_coord new file mode 100644 index 000000000..fb8c5a8df --- /dev/null +++ b/tests/abacus.md/Si_coord @@ -0,0 +1,10 @@ +0 0 0 +1.30082342 1.37638993 1.3547995 +5.35320953 2.72430477 2.68504527 +1.35126946 1.34726983 1.3286265 +2.70155326 2.69533522 5.35848569 +1.30969169 1.37268717 1.3150785 +2.66403555 0.02130293 2.64633444 +1.35284016 1.34443879 1.29061924 +2.70202696 2.69316139 5.32175227 +1.31985538 1.36795346 1.2771711 diff --git a/tests/abacus.md/Si_force b/tests/abacus.md/Si_force new file mode 100644 index 000000000..b22dd3cc1 --- /dev/null +++ b/tests/abacus.md/Si_force @@ -0,0 +1,10 @@ +-0.885363 0.500467 0.15024 +0.885363 -0.500467 -0.15024 +0.830073 -0.488698 -0.076368 +-0.830073 0.488698 0.076368 +-0.774114 0.493555 0.132287 +0.774114 -0.493555 -0.132287 +0.685454 -0.466777 -0.074732 +-0.685454 0.466777 0.074732 +-0.597076 0.44338 0.09741 +0.597076 -0.44338 -0.09741 diff --git a/tests/abacus.md/Si_virial b/tests/abacus.md/Si_virial new file mode 100644 index 000000000..8ee021799 --- /dev/null +++ b/tests/abacus.md/Si_virial @@ -0,0 +1,15 @@ +-3.01924575 0.09342813 0.33227574 +0.09342813 -3.05301021 -0.59008156 +0.33227574 -0.59008156 -3.06760338 +-3.02007615 -0.05764851 -0.32736857 +-0.05764851 -3.0485708 0.55474523 +-0.32736857 0.55474523 -3.06346952 +-3.02121465 0.08230513 0.32783898 +0.08230513 -3.04371791 -0.51561023 +0.32783898 -0.51561023 -3.05814259 +-3.02169395 -0.05491244 -0.31223515 +-0.05491244 -3.03763085 0.45779192 +-0.31223515 0.45779192 -3.05114849 +-3.02170837 0.0607685 0.29473041 +0.0607685 -3.03181773 -0.39741107 +0.29473041 -0.39741107 -3.04370231 diff --git a/tests/test_abacus_md.py b/tests/test_abacus_md.py new file mode 100644 index 000000000..1ce7cf8d0 --- /dev/null +++ b/tests/test_abacus_md.py @@ -0,0 +1,86 @@ +import os +import numpy as np +import unittest +from context import dpdata +from dpdata.unit import LengthConversion + +bohr2ang = LengthConversion("bohr", "angstrom").value() + +class TestABACUSMD: + + def test_atom_names(self) : + self.assertEqual(self.system_Si.data['atom_names'], ['Si']) + #self.assertEqual(self.system_h2o.data['atom_names'], ['O','H']) + + def test_atom_numbs(self) : + self.assertEqual(self.system_Si.data['atom_numbs'], [2]) + #self.assertEqual(self.system_h2o.data['atom_numbs'], [64,128]) + + def test_atom_types(self) : + ref_type = [0, 0] + ref_type = np.array(ref_type) + for ii in range(ref_type.shape[0]) : + self.assertEqual(self.system_Si.data['atom_types'][ii], ref_type[ii]) + + def test_cell(self) : + cell = bohr2ang * 10.2 * np.array([[0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]]) + for idx in range(np.shape(self.system_Si.data['cells'])[0]): + for ii in range(cell.shape[0]) : + for jj in range(cell.shape[1]) : + self.assertAlmostEqual(self.system_Si.data['cells'][idx][ii][jj], cell[ii][jj]) + + def test_coord(self) : + fp = open('abacus.md/Si_coord') + coord = [] + for ii in fp : + coord.append([float(jj) for jj in ii.split()]) + coord = np.array(coord) + coord = coord.reshape([5, 2, 3]) + for ii in range(coord.shape[0]) : + for jj in range(coord.shape[1]) : + for kk in range(coord.shape[2]): + self.assertAlmostEqual(self.system_Si.data['coords'][ii][jj][kk], coord[ii][jj][kk]) + fp.close() + + def test_force(self) : + fp = open('abacus.md/Si_force') + force = [] + for ii in fp : + force.append([float(jj) for jj in ii.split()]) + force = np.array(force) + force = force.reshape([5, 2, 3]) + for ii in range(force.shape[0]) : + for jj in range(force.shape[1]) : + for kk in range(force.shape[2]): + self.assertAlmostEqual(self.system_Si.data['forces'][ii][jj][kk], force[ii][jj][kk]) + fp.close() + + def test_virial(self) : + fp = open('abacus.md/Si_virial') + virial = [] + for ii in fp : + virial.append([float(jj) for jj in ii.split()]) + virial = np.array(virial) + virial = virial.reshape([5, 3, 3]) + for ii in range(virial.shape[0]) : + for jj in range(virial.shape[1]) : + for kk in range(virial.shape[2]) : + self.assertAlmostEqual(self.system_Si.data['virials'][ii][jj][kk], virial[ii][jj][kk]) + fp.close() + + def test_energy(self) : + ref_energy = np.array([-211.77183266, -211.7739761 , -211.77713677, -211.78079673, + -211.78511428]) + for ii in range(5): + self.assertAlmostEqual(self.system_Si.data['energies'][ii], ref_energy[ii]) + + +class TestABACUSMDLabeledOutput(unittest.TestCase, TestABACUSMD): + + def setUp(self): + self.system_Si = dpdata.LabeledSystem('abacus.md',fmt='abacus/md') + # self.system_h2o = dpdata.LabeledSystem('qe.scf/02.out',fmt='qe/pw/scf') + + +if __name__ == '__main__': + unittest.main() \ No newline at end of file