added examples/pmd_parallel and corrected nap/makefile.

examples/pmd_parallel/in.params.Coulomb

@@ -0,0 +1,17 @@
+terms   screened_cut
+charges   fixed_bvs 
+   O       -2.0   0.66    2
+   Li       1.0   1.28    2
+   La       3.0   2.07    6
+   Zr       4.0   1.75    5
+
+fbvs   1.000
+
+interactions 
+   O   O
+   Li  Li
+   Li  La
+   Li  Zr
+   La  La
+   La  Zr
+   Zr  Zr

examples/pmd_parallel/in.params.Morse

@@ -0,0 +1,4 @@
+# cspi, cspj,    D,      alpha,  rmin
+   O    Li  0.98816  1.93798  1.94001
+   O    La  1.18587  2.21730  2.46989
+   O    Zr  2.19103  2.04082  1.99602

examples/pmd_parallel/in.pmd

@@ -0,0 +1,33 @@
+!
+!  unit of time  = femto sec
+!  unit of length= Angstrom
+!  unit of mass  = unified atomic mass unit
+!
+
+io_format    ascii
+
+time_interval     1d0
+num_iteration     2
+num_out_energy    100
+
+flag_out_pmd      2
+num_out_pmd       10
+
+force_type        Coulomb Morse
+cutoff_radius     6.0d0
+cutoff_buffer     0.3d0
+flag_coulomb      1
+
+flag_damping      0
+damping_coeff     0.99d0
+
+initial_temperature     -300d0
+temperature_control     none
+temperature_target      1 100d0
+temperature_relax_time  100d0
+
+factor_direction 3 2
+  1.000d0  1.000d0  1.000d0
+  1.000d0  0.000d0  1.000d0
+
+flag_compute_stress   T

examples/pmd_parallel/makefile

@@ -0,0 +1,27 @@
+.phony: clean veryclean keep test
+
+clean:
+	rm -f dump_* erg.pmd frc.pmd strs.pmd *~
+
+veryclean: clean
+	rm -f out.erg out.pmd.{2,4,8} pmdfin
+
+test:
+	@mpirun --oversubscribe -np 2 ../../pmd/pmd 2>&1 > out.pmd.2
+	@mpirun --oversubscribe -np 4 ../../pmd/pmd 2>&1 > out.pmd.4
+	@mpirun --oversubscribe -np 8 ../../pmd/pmd 2>&1 > out.pmd.8
+	@grep Potential out.pmd.REF | tail -n1 > /tmp/out.REF
+	@grep Potential out.pmd.2 | tail -n1 > /tmp/out.2
+	@grep Potential out.pmd.4 | tail -n1 > /tmp/out.4
+	@grep Potential out.pmd.8 | tail -n1 > /tmp/out.8
+	@diff -q /tmp/out.2 /tmp/out.REF > /dev/null || (echo " FAIL: parallel 2 in examples/pmd_parallel" && exit 1)
+	@echo " PASS: parallel 2 in examples/pmd_parallel"
+	@diff -q /tmp/out.4 /tmp/out.REF > /dev/null || (echo " FAIL: parallel 4 in examples/pmd_parallel" && exit 1)
+	@echo " PASS: parallel 4 in examples/pmd_parallel"
+	@diff -q /tmp/out.8 /tmp/out.REF > /dev/null || (echo " FAIL: parallel 8 in examples/pmd_parallel" && exit 1)
+	@echo " PASS: parallel 8 in examples/pmd_parallel"
+
+resdir := result_$(shell date "+%y%m%d_%H%M")
+keep:
+	mkdir -p $(resdir)
+	cp in.* out.* pmdini pmdfin $(resdir)/

examples/pmd_parallel/out.pmd.REF

@@ -0,0 +1,169 @@
+========================================================================
+ PMD: A Parallel Molecular Dynamics program 
+
+ Revision: rev200428
+ Contributors: 
+   - Ryo KOBAYASHI <kobayashi.ryo@nitech.ac.jp>
+========================================================================
+
+ Job started at 10:58:22 on 2021-01-09
+
+ Read pmdini in ascii mode.
+ Species order read from pmdini option: 
+    1:    O
+    2:   Li
+    3:   La
+    4:   Zr
+
+ Lattice vectors:
+   a = [       13.239       0.000       0.000 ]
+   b = [        0.000      13.239       0.000 ]
+   c = [        0.000       0.000      12.765 ]
+ Lattice parameters:
+   |a| =     13.239 Ang.,  alpha =   90.00 deg.
+   |b| =     13.239 Ang.,  beta  =   90.00 deg.
+   |c| =     12.765 Ang.,  gamma =   90.00 deg.
+ Cell volume = 2237.44 Ang^3
+ Number of each species in the initial configuration
+   O  :  96
+   Li :  56
+   La :  24
+   Zr :  16
+
+ Number of processes in MPI = 1
+
+------------------------------------------------------------------------
+           Initial setting   
+------------------------------------------------------------------------
+  num_nodes_x     -1
+  num_nodes_y     -1
+  num_nodes_z     -1
+
+  io_format     ascii 
+  print_level     1
+
+  time_interval     1.000
+  num_iteration     2
+  num_out_energy     100
+
+  flag_out_pmd     2
+  num_out_pmd     10
+  dump_aux_order    ekin epot sxx syy szz syz sxz sxy 
+
+  force_type     Coulomb  Morse
+  cutoff_radius      6.000
+  cutoff_buffer      0.300
+
+  flag_damping     0
+  damping_coeff     .9900
+  converge_eps     .0001
+  converge_num     1
+  min_iteration     0
+
+  temperature_control     none
+  initial_temperature      -300.00
+  remove_translation     0
+
+  stress_control     none
+
+  zload_type     none
+
+  factor_direction
+       0   0.000   0.000   0.000
+       1   1.000   1.000   1.000
+       2   1.000   0.000   1.000
+       3   1.000   1.000   1.000
+       4   1.000   1.000   1.000
+       5   1.000   1.000   1.000
+       6   1.000   1.000   1.000
+       7   1.000   1.000   1.000
+       8   1.000   1.000   1.000
+       9   1.000   1.000   1.000
+
+  mass
+       1 O     15.9990
+       2 Li     6.9400
+       3 La   138.9000
+       4 Zr    91.2240
+
+  boundary     ppp
+
+------------------------------------------------------------------------
+
+ Broadcast data to be shared with all the nodes.
+ Number of spatial divisions automatically set, NX,NY,NZ= 1 1 1
+
+ Ensemble = NVE
+
+ Number of ifmvs = 1
+ rcut, rbuf =  6.000 0.300
+ Min number of local atoms =        192
+ Max number of local atoms =        192
+   nbmax =      10000
+   namax = nalmax*1.2 + nbmax  =      10230
+   nnmax =        100
+ Memory for main routine   =          8 MByte
+
+ Number of total atoms = 192
+ Number of species     = 4
+ Degrees of freedom for each ifmv =  576  0  0  0  0  0  0  0  0
+
+ Use the following force-fields:  Coulomb  Morse 
+
+ Coulomb parameters:
+   csp,vid,rad,npq =    O -2.000  0.660   2
+   csp,vid,rad,npq =   Li  1.000  1.280   2
+   csp,vid,rad,npq =   La  3.000  2.070   6
+   csp,vid,rad,npq =   Zr  4.000  1.750   5
+   cspi,cspj,rho_bvs=     O    O    1.3200
+   cspi,cspj,rho_bvs=    Li   Li    2.5600
+   cspi,cspj,rho_bvs=    Li   La    3.3500
+   cspi,cspj,rho_bvs=    Li   Zr    3.0300
+   cspi,cspj,rho_bvs=    La   La    4.1400
+   cspi,cspj,rho_bvs=    La   Zr    3.8200
+   cspi,cspj,rho_bvs=    Zr   Zr    3.5000
+ Finished reading ./in.params.Coulomb
+
+ Morse parameters:
+   cspi,cspj,D,alpha,rmin =    O  Li  0.988  1.938  1.940
+   cspi,cspj,D,alpha,rmin =    O  La  1.186  2.217  2.470
+   cspi,cspj,D,alpha,rmin =    O  Zr  2.191  2.041  1.996
+ ================= WORNING =======================
+   nnmax is less than 5*(num of atoms in a cell)
+   You should set max_num_meighbors greater than 100
+ =================================================
+ Max num of neighbors at 1st call = 98
+
+ Charges fixed from ideal valences and composition:
+   csp, V_ideal, V_actual =    O -2.000 -1.199
+   csp, V_ideal, V_actual =   Li  1.000  0.834
+   csp, V_ideal, V_actual =   La  3.000  1.444
+   csp, V_ideal, V_actual =   Zr  4.000  2.110
+
+ Ewald energy term by term:
+   Self term         =       0.0000 eV
+   Short-range term  =     533.0033 eV
+   Long-range term   =       0.0000 eV
+
+ Initial values:
+   Kinetic energy  =          7.58973 eV =      0.040 eV/atom
+   Potential energy=       -161.24366 eV =     -0.840 eV/atom
+   Temperature 1   =        307.41779 K
+   Temperature     =        307.41779 K
+   Pressure        =         24.84780 GPa (compressive)
+   Stress tensor   = 25.589 25.670 23.285 -.025 -.029 .006
+
+ istp,etime,temp,epot,vol,prss= 0        0.01      307.42  -1.6124E+02  2.237E+03  2.485E+01
+ istp,etime,temp,epot,vol,prss= 1        0.01      311.04  -1.6133E+02  2.237E+03  2.485E+01
+ istp,etime,temp,epot,vol,prss= 2        0.01      318.59  -1.6152E+02  2.237E+03  2.483E+01
+
+ Final values:
+   Kinetic energy  =          7.86560 eV =      0.041 eV/atom
+   Potential energy=       -161.51956 eV =     -0.841 eV/atom
+   Temperature 1   =        318.59178 K
+   Temperature     =        318.59178 K
+   Pressure        =         24.83214 GPa (compressive)
+
+ Time                  =       0.01 sec  =   0h00m00s
+
+ Job finished at 10:58:22 on 2021-01-09