Added additional tutorials for the dynamical matrix calculator

examples/USER/phonon/dynamical_matrix_command/GaAs/GaAs.py

@@ -0,0 +1,39 @@
+from ase import Atoms, Atom
+from ase.calculators.lammpslib import LAMMPSlib
+import numpy as np
+import matplotlib.pyplot as plt
+from mpi4py import MPI
+
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+
+GaAs = Atoms([Atom('Ga', (0.0, 0.0, 0.0)),
+              Atom('As', (1.413425, 1.413425, 1.413425))],
+             cell=[(0.0, 2.82685, 2.82685), (2.82685, 0.0, 2.82685), (2.82685, 2.82685, 0.0)],
+             pbc=True,)
+
+cmds = ["pair_style bop", "pair_coeff * * ../../../../../potentials/GaAs.bop.table Ga As",
+        "comm_modify cutoff 12"]
+
+mends = ["info system",
+         "dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
+         "neigh_modify delay 0"]
+
+N = 5
+GaAs = GaAs.repeat([N, N, N])
+
+lammps = LAMMPSlib(lmpcmds=cmds, atom_types={'Ga': 1, 'As': 2}, amendments=mends, log_file='lammps.log')
+
+GaAs.set_calculator(lammps)
+GaAs.get_potential_energy()
+
+if rank == 0:
+    dynmat = np.loadtxt("dynmat.dat")
+    dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
+    eigv = np.linalg.eigvals(dynmat)
+    eigv.sort()
+    eigv = np.sqrt(np.abs(eigv))/(2*np.pi)
+    plt.hist(eigv, 80)
+    plt.xlabel('Frequency (THz)')
+    plt.show()
+

examples/USER/phonon/dynamical_matrix_command/GaN/GaN.py

@@ -0,0 +1,39 @@
+from ase import Atoms, Atom
+from ase.calculators.lammpslib import LAMMPSlib
+import numpy as np
+import matplotlib.pyplot as plt
+from mpi4py import MPI
+
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+
+GaN = Atoms([Atom('Ga', (1.59, 0.917986928012, 0.0)),
+             Atom('Ga', (1.59, -0.917986928012, 2.583)),
+             Atom('N', (1.59, 0.917986928012, 1.98891)),
+             Atom('N', (1.59, -0.917986928012, 4.57191))],
+            cell=[(1.59, -2.75396078403, 0.0), (1.59, 2.75396078403, 0.0), (0.0, 0.0, 5.166)],
+            pbc=True)
+
+cmds = ["pair_style tersoff", "pair_coeff * * ../../../../../potentials/GaN.tersoff Ga N"]
+
+mends = ["info system",
+         "dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
+         "neigh_modify delay 0"]
+
+N = 6
+GaN = GaN.repeat([N, N, N])
+
+lammps = LAMMPSlib(lmpcmds=cmds, atom_types={'Ga': 1, 'N': 2}, amendments=mends, log_file='lammps.log')
+
+GaN.set_calculator(lammps)
+GaN.get_potential_energy()
+
+if rank == 0:
+    dynmat = np.loadtxt("dynmat.dat")
+    dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
+    eigv = np.linalg.eigvals(dynmat)
+    eigv.sort()
+    eigv = np.sqrt(np.abs(eigv))/(2*np.pi)
+    plt.hist(eigv, 80)
+    plt.xlabel('Frequency (THz)')
+    plt.show()

examples/USER/phonon/dynamical_matrix_command/Quartz/quartz.py

@@ -0,0 +1,57 @@
+from ase import Atoms, Atom
+from ase.calculators.lammpslib import LAMMPSlib
+import numpy as np
+import matplotlib.pyplot as plt
+from mpi4py import MPI
+
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+
+quartz = Atoms(
+    [Atom('Si', (1.1545226, -1.99969180169, 0.0)),
+     Atom('Si', (1.1545226, 1.99969180169, 3.6036)),
+     Atom('Si', (2.6069548, 2.15247249027e-16, 1.8018)),
+     Atom('O', (1.6724232, -0.624132037742, 0.64378314)),
+     Atom('O', (1.6724232, 0.624132037742, 2.9598186618)),
+     Atom('O', (2.1623026, -2.49695388906, 4.2473849418)),
+     Atom('O', (3.5392742, 1.13629495821, 1.1580150582)),
+     Atom('O', (3.5392742, -1.13629495821, 2.4455813382)),
+     Atom('O', (2.1623026, 2.49695388906, 4.76161686))],
+    cell=[(2.458, -4.257380885, 0.0), (2.458, 4.257380885, 0.0), (0.0, 0.0, 5.4054)],
+    pbc=True,
+    )
+
+# number of repeats
+N = 3
+quartz = quartz.repeat([N, N, N])
+
+header = ['units metal',
+          'atom_style charge',
+          'atom_modify map array sort 0 0']
+
+cmds = ["pair_style      buck/coul/long 10.0 8.0",
+        "pair_coeff	1 1      0      1         0",
+        "pair_coeff	1 2   18003.7572 0.20520 133.5381",
+        "pair_coeff	2 2    1388.7730 0.36232 175.0000",
+        "kspace_style ewald 1.0e-12",
+        "set type 1 charge 2.4",
+        "set type 2 charge -1.2"]
+
+mends = ["dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
+         "neigh_modify delay 0"]
+
+
+lammps = LAMMPSlib(lmpcmds=cmds, lammps_header=header, amendments=mends, log_file='lammps.log')
+
+quartz.set_calculator(lammps)
+quartz.get_potential_energy()
+
+if rank == 0:
+    dynmat = np.loadtxt("dynmat.dat")
+    dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
+    eigv = np.linalg.eigvals(dynmat)
+    eigv.sort()
+    plt.hist(33*np.sqrt(np.abs(eigv))/(2*np.pi), 80)
+    plt.xlabel('Frequency (cm-1)')
+    plt.show()
+

examples/USER/phonon/dynamical_matrix_command/Silicon/README.md

@@ -7,7 +7,7 @@ This directory contains the ingredients to calculate a dynamical matrix.
 Example:
 ```
 NP=4 #number of processors
-mpirun -np $NP lmp_mpi < in.silicon > out.silicon
+mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
 ```
 
 To test out a different silicon example:
@@ -15,7 +15,7 @@ To test out a different silicon example:
 LMP_FILE=amorphous_silicon.lmp
 cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
 NP=4 #number of processors
-mpirun -np $NP lmp_mpi < in.silicon > out.silicon
+mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
 ```
 
 ## Requires: MANYBODY and MOLECULE packages

examples/USER/phonon/third_order_command/silicon/README.md

@@ -8,7 +8,7 @@ Example:
 ```
 $THIRD_ORDER=third_order #tensor output file
 NP=4 #number of processors
-mpirun -np $NP lmp_mpi < in.silicon > out.silicon
+mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
 combine.sh third_order
 ```
 
@@ -18,7 +18,7 @@ $THIRD_ORDER=third_order
 $LMP_FILE=amorphous_silicon.lmp
 cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
 NP=4 #number of processors
-mpirun -np $NP lmp_mpi < in.silicon > out.silicon
+mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
 bash combine.sh $THIRD_ORDER
 ```
 

src/USER-PHONON/third_order.cpp

@@ -168,13 +168,11 @@ void ThirdOrder::options(int narg, char **arg)
     if (narg < 0) error->all(FLERR,"Illegal dynamical_matrix command");
     int iarg = 0;
     const char *filename = "third_order.txt";
-    std::stringstream fss;
 
     while (iarg < narg) {
         if (strcmp(arg[iarg],"file") == 0) {
             if (iarg+2 > narg) error->all(FLERR, "Illegal dynamical_matrix command");
-            fss << arg[iarg + 1] << me;
-            filename = fss.str().c_str();
+            filename = arg[iarg + 1];
             file_flag = 1;
             iarg += 2;
         }
@@ -189,7 +187,7 @@ void ThirdOrder::options(int narg, char **arg)
             iarg += 2;
         } else error->all(FLERR,"Illegal dynamical_matrix command");
     }
-    if (file_flag == 1 and me == 0) {
+    if (file_flag == 1 && me == 0) {
         openfile(filename);
     }
 }
@@ -338,10 +336,9 @@ void ThirdOrder::writeMatrix(double *dynmat, int i, int a, int j, int b)
     if (!binaryflag && fp) {
         clearerr(fp);
         for (int k = 0; k < gcount; k++){
-            double norm = pow(dynmat[k*3], 2)
-                          + pow(dynmat[k*3+1], 2)
-                          + pow(dynmat[k+3+2], 2);
-            if (norm > 1.0e-16)
+            if (dynmat[k*3] > 1.0e-16
+                && dynmat[k*3+1] > 1.0e-16
+                && dynmat[k*3+2] > 1.0e-16)
                 fprintf(fp,
                         "%d %d %d %d %d %7.8f %7.8f %7.8f\n",
                         i+1, a + 1, j+1, b + 1, groupmap[k]+1,