Paper updates (#88)

* docs

* docs update

* docs update

* docs update

* use forward euler to simple build works

* Update README.md

* Update README.md

* Update README.md

* whitespace

* enable DMI and anis in scaling test

* skyrmion diagnostic post processing utility

* renname file

* restart bugfix

* sundials 7.1.1

* inputs file for paper demag plot

* license and copyright

* patches to get regression tests running again
some benchmarks will be changing

* fix sundials settings

* cleanup per Weiqun

* logic for different physics wasn't right for single-rate case

* add SUNDIALS_HOME

* sundials update

* comments in inputs file

* scaling tests

* turn on RK4 for STD3

* tweaks for final paper

* bugfix - for hysteresis do not compute Hbias each time step!!!

* fix std2 inputs to match text in paper (and get proper results)

* fix up DMI1 problem

* paper update

Author: ajnonaka

Exec/DMI_diagnostic/DMI_diagnostic.cpp

@@ -118,10 +118,10 @@ main (int   argc,
             int k = (hi.z+1)/2;
             int j = (hi.y+1)/2;
             for (auto i = (hi.x+1)/2; i <= hi.x; ++i) {
-                std::cout << i << " " << mfdata(i,j,k,3)/1.1e6 << " " << mfdata(i,j,k,16)+offset << "\n";
+                std::cout << i << " " << mfdata(i,j,k,2)/1.1e6 << " " << mfdata(i,j,k,3)+offset << "\n";
                 // 2pi cyclic fix
                 if (i<hi.x) {
-                    if (offset==0. && mfdata(i,j,k,16)>5. && mfdata(i+1,j,k,16)<1.) {
+                    if (offset==0. && mfdata(i,j,k,3)>5. && mfdata(i+1,j,k,3)<1.) {
                         offset = 2.*M_PI;
                     }
                 }

Exec/scaling_inputs/inputs_scaling_cpu_0.25

@@ -0,0 +1,52 @@
+amrex.use_gpu_aware_mpi=1
+
+n_cell = 128 128 128
+max_grid_size_x = 32
+max_grid_size_y = 32
+max_grid_size_z = 64
+
+dt = 1.e-15
+nsteps = 100
+plot_int = -1
+chk_int = -1
+restart = -1
+
+prob_lo = 0. 0. 0.
+prob_hi = 512.e-9 512.e-9 512.e-9
+
+mu0 = 1.25663e-6
+
+Mx_parser(x,y,z) = "8.e5 * (x>0.)*(x<512.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9)"
+My_parser(x,y,z) = "0."
+Mz_parser(x,y,z) = "0."
+
+# Field 1:  mu_0 Hx=-24.6 mT, mu_0 Hy= 4.3 mT, mu_0 Hz= 0.0 mT
+# which is a field approximately 25 mT, directed 170 degrees counterclockwise from the positive x axis
+timedependent_Hbias = 0
+Hx_bias_parser(x,y,z,t) = "1.e5"
+Hy_bias_parser(x,y,z,t) = "1.e5"
+Hz_bias_parser(x,y,z,t) = "1.e5"
+
+timedependent_alpha = 0
+alpha_parser(x,y,z,t) =    "(x>0.)*(x<512.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 0.5"
+Ms_parser(x,y,z) =         "(x>0.)*(x<512.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 8.e5"
+gamma_parser(x,y,z) =      "(x>0.)*(x<512.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -1.759e11"
+exchange_parser(x,y,z) =   "(x>0.)*(x<512.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 1.3e-11"
+anisotropy_parser(x,y,z) = "(x>0.)*(x<512.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -139.26"
+DMI_parser(x,y,z) =        "(x>0.)*(x<512.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -4.5e-3"
+
+precession = 1
+demag_coupling = 1
+FFT_solver = 1
+M_normalization = 1  # 0 = unsaturated case; 1 = saturated case
+exchange_coupling = 1
+anisotropy_coupling = 1
+anisotropy_axis = 0.0 0.0 1.0
+DMI_coupling = 1
+
+# INTEGRATION
+
+TimeIntegratorOption = 1 #Forward Euler
+
+integration.type = RungeKutta
+integration.rk.type = 1

Exec/scaling_inputs/inputs_scaling_cpu_0.5

@@ -0,0 +1,52 @@
+amrex.use_gpu_aware_mpi=1
+
+n_cell = 256 128 128
+max_grid_size_x = 32
+max_grid_size_y = 32
+max_grid_size_z = 64
+
+dt = 1.e-15
+nsteps = 100
+plot_int = -1
+chk_int = -1
+restart = -1
+
+prob_lo = 0. 0. 0.
+prob_hi = 1024.e-9 512.e-9 512.e-9
+
+mu0 = 1.25663e-6
+
+Mx_parser(x,y,z) = "8.e5 * (x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9)"
+My_parser(x,y,z) = "0."
+Mz_parser(x,y,z) = "0."
+
+# Field 1:  mu_0 Hx=-24.6 mT, mu_0 Hy= 4.3 mT, mu_0 Hz= 0.0 mT
+# which is a field approximately 25 mT, directed 170 degrees counterclockwise from the positive x axis
+timedependent_Hbias = 0
+Hx_bias_parser(x,y,z,t) = "1.e5"
+Hy_bias_parser(x,y,z,t) = "1.e5"
+Hz_bias_parser(x,y,z,t) = "1.e5"
+
+timedependent_alpha = 0
+alpha_parser(x,y,z,t) =    "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 0.5"
+Ms_parser(x,y,z) =         "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 8.e5"
+gamma_parser(x,y,z) =      "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -1.759e11"
+exchange_parser(x,y,z) =   "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 1.3e-11"
+anisotropy_parser(x,y,z) = "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -139.26"
+DMI_parser(x,y,z) =        "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -4.5e-3"
+
+precession = 1
+demag_coupling = 1
+FFT_solver = 1
+M_normalization = 1  # 0 = unsaturated case; 1 = saturated case
+exchange_coupling = 1
+anisotropy_coupling = 1
+anisotropy_axis = 0.0 0.0 1.0
+DMI_coupling = 1
+
+# INTEGRATION
+
+TimeIntegratorOption = 1 #Forward Euler
+
+integration.type = RungeKutta
+integration.rk.type = 1

Exec/scaling_inputs/inputs_scaling_cpu_1

@@ -0,0 +1,52 @@
+amrex.use_gpu_aware_mpi=1
+
+n_cell = 256 256 128
+max_grid_size_x = 32
+max_grid_size_y = 32
+max_grid_size_z = 64
+
+dt = 1.e-15
+nsteps = 100
+plot_int = -1
+chk_int = -1
+restart = -1
+
+prob_lo = 0. 0. 0.
+prob_hi = 1024.e-9 1024.e-9 512.e-9
+
+mu0 = 1.25663e-6
+
+Mx_parser(x,y,z) = "8.e5 * (x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<512.e-9)"
+My_parser(x,y,z) = "0."
+Mz_parser(x,y,z) = "0."
+
+# Field 1:  mu_0 Hx=-24.6 mT, mu_0 Hy= 4.3 mT, mu_0 Hz= 0.0 mT
+# which is a field approximately 25 mT, directed 170 degrees counterclockwise from the positive x axis
+timedependent_Hbias = 0
+Hx_bias_parser(x,y,z,t) = "1.e5"
+Hy_bias_parser(x,y,z,t) = "1.e5"
+Hz_bias_parser(x,y,z,t) = "1.e5"
+
+timedependent_alpha = 0
+alpha_parser(x,y,z,t) =    "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<512.e-9) * 0.5"
+Ms_parser(x,y,z) =         "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<512.e-9) * 8.e5"
+gamma_parser(x,y,z) =      "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<512.e-9) * -1.759e11"
+exchange_parser(x,y,z) =   "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<512.e-9) * 1.3e-11"
+anisotropy_parser(x,y,z) = "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<512.e-9) * -139.26"
+DMI_parser(x,y,z) =        "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<512.e-9) * -4.5e-3"
+
+precession = 1
+demag_coupling = 1
+FFT_solver = 1
+M_normalization = 1  # 0 = unsaturated case; 1 = saturated case
+exchange_coupling = 1
+anisotropy_coupling = 1
+anisotropy_axis = 0.0 0.0 1.0
+DMI_coupling = 1
+
+# INTEGRATION
+
+TimeIntegratorOption = 1 #Forward Euler
+
+integration.type = RungeKutta
+integration.rk.type = 1

Exec/scaling_inputs/inputs_scaling_cpu_128

@@ -0,0 +1,52 @@
+amrex.use_gpu_aware_mpi=1
+
+n_cell = 1024 1024 1024
+max_grid_size_x = 32
+max_grid_size_y = 32
+max_grid_size_z = 64
+
+dt = 1.e-15
+nsteps = 100
+plot_int = -1
+chk_int = -1
+restart = -1
+
+prob_lo = 0. 0. 0.
+prob_hi = 4096.e-9 4096.e-9 4096.e-9
+
+mu0 = 1.25663e-6
+
+Mx_parser(x,y,z) = "8.e5 * (x>0.)*(x<4096.e-9)*(y>0.)*(y<4096.e-9)*(z>0.)*(z<4096.e-9)"
+My_parser(x,y,z) = "0."
+Mz_parser(x,y,z) = "0."
+
+# Field 1:  mu_0 Hx=-24.6 mT, mu_0 Hy= 4.3 mT, mu_0 Hz= 0.0 mT
+# which is a field approximately 25 mT, directed 170 degrees counterclockwise from the positive x axis
+timedependent_Hbias = 0
+Hx_bias_parser(x,y,z,t) = "1.e5"
+Hy_bias_parser(x,y,z,t) = "1.e5"
+Hz_bias_parser(x,y,z,t) = "1.e5"
+
+timedependent_alpha = 0
+alpha_parser(x,y,z,t) =    "(x>0.)*(x<4096.e-9)*(y>0.)*(y<4096.e-9)*(z>0.)*(z<4096.e-9) * 0.5"
+Ms_parser(x,y,z) =         "(x>0.)*(x<4096.e-9)*(y>0.)*(y<4096.e-9)*(z>0.)*(z<4096.e-9) * 8.e5"
+gamma_parser(x,y,z) =      "(x>0.)*(x<4096.e-9)*(y>0.)*(y<4096.e-9)*(z>0.)*(z<4096.e-9) * -1.759e11"
+exchange_parser(x,y,z) =   "(x>0.)*(x<4096.e-9)*(y>0.)*(y<4096.e-9)*(z>0.)*(z<4096.e-9) * 1.3e-11"
+anisotropy_parser(x,y,z) = "(x>0.)*(x<4096.e-9)*(y>0.)*(y<4096.e-9)*(z>0.)*(z<4096.e-9) * -139.26"
+DMI_parser(x,y,z) =        "(x>0.)*(x<4096.e-9)*(y>0.)*(y<4096.e-9)*(z>0.)*(z<4096.e-9) * -4.5e-3"
+
+precession = 1
+demag_coupling = 1
+FFT_solver = 1
+M_normalization = 1  # 0 = unsaturated case; 1 = saturated case
+exchange_coupling = 1
+anisotropy_coupling = 1
+anisotropy_axis = 0.0 0.0 1.0
+DMI_coupling = 1
+
+# INTEGRATION
+
+TimeIntegratorOption = 1 #Forward Euler
+
+integration.type = RungeKutta
+integration.rk.type = 1

Exec/scaling_inputs/inputs_scaling_cpu_16

@@ -0,0 +1,52 @@
+amrex.use_gpu_aware_mpi=1
+
+n_cell = 512 512 512
+max_grid_size_x = 32
+max_grid_size_y = 32
+max_grid_size_z = 64
+
+dt = 1.e-15
+nsteps = 100
+plot_int = -1
+chk_int = -1
+restart = -1
+
+prob_lo = 0. 0. 0.
+prob_hi = 2048.e-9 2048.e-9 2048.e-9
+
+mu0 = 1.25663e-6
+
+Mx_parser(x,y,z) = "8.e5 * (x>0.)*(x<2048.e-9)*(y>0.)*(y<2048.e-9)*(z>0.)*(z<2048.e-9)"
+My_parser(x,y,z) = "0."
+Mz_parser(x,y,z) = "0."
+
+# Field 1:  mu_0 Hx=-24.6 mT, mu_0 Hy= 4.3 mT, mu_0 Hz= 0.0 mT
+# which is a field approximately 25 mT, directed 170 degrees counterclockwise from the positive x axis
+timedependent_Hbias = 0
+Hx_bias_parser(x,y,z,t) = "1.e5"
+Hy_bias_parser(x,y,z,t) = "1.e5"
+Hz_bias_parser(x,y,z,t) = "1.e5"
+
+timedependent_alpha = 0
+alpha_parser(x,y,z,t) =    "(x>0.)*(x<2048.e-9)*(y>0.)*(y<2048.e-9)*(z>0.)*(z<2048.e-9) * 0.5"
+Ms_parser(x,y,z) =         "(x>0.)*(x<2048.e-9)*(y>0.)*(y<2048.e-9)*(z>0.)*(z<2048.e-9) * 8.e5"
+gamma_parser(x,y,z) =      "(x>0.)*(x<2048.e-9)*(y>0.)*(y<2048.e-9)*(z>0.)*(z<2048.e-9) * -1.759e11"
+exchange_parser(x,y,z) =   "(x>0.)*(x<2048.e-9)*(y>0.)*(y<2048.e-9)*(z>0.)*(z<2048.e-9) * 1.3e-11"
+anisotropy_parser(x,y,z) = "(x>0.)*(x<2048.e-9)*(y>0.)*(y<2048.e-9)*(z>0.)*(z<2048.e-9) * -139.26"
+DMI_parser(x,y,z) =        "(x>0.)*(x<2048.e-9)*(y>0.)*(y<2048.e-9)*(z>0.)*(z<2048.e-9) * -4.5e-3"
+
+precession = 1
+demag_coupling = 1
+FFT_solver = 1
+M_normalization = 1  # 0 = unsaturated case; 1 = saturated case
+exchange_coupling = 1
+anisotropy_coupling = 1
+anisotropy_axis = 0.0 0.0 1.0
+DMI_coupling = 1
+
+# INTEGRATION
+
+TimeIntegratorOption = 1 #Forward Euler
+
+integration.type = RungeKutta
+integration.rk.type = 1

Exec/scaling_inputs/inputs_scaling_cpu_2

@@ -0,0 +1,52 @@
+amrex.use_gpu_aware_mpi=1
+
+n_cell = 256 256 256
+max_grid_size_x = 32
+max_grid_size_y = 32
+max_grid_size_z = 64
+
+dt = 1.e-15
+nsteps = 100
+plot_int = -1
+chk_int = -1
+restart = -1
+
+prob_lo = 0. 0. 0.
+prob_hi = 1024.e-9 1024.e-9 1024.e-9
+
+mu0 = 1.25663e-6
+
+Mx_parser(x,y,z) = "8.e5 * (x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<1024.e-9)"
+My_parser(x,y,z) = "0."
+Mz_parser(x,y,z) = "0."
+
+# Field 1:  mu_0 Hx=-24.6 mT, mu_0 Hy= 4.3 mT, mu_0 Hz= 0.0 mT
+# which is a field approximately 25 mT, directed 170 degrees counterclockwise from the positive x axis
+timedependent_Hbias = 0
+Hx_bias_parser(x,y,z,t) = "1.e5"
+Hy_bias_parser(x,y,z,t) = "1.e5"
+Hz_bias_parser(x,y,z,t) = "1.e5"
+
+timedependent_alpha = 0
+alpha_parser(x,y,z,t) =    "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<1024.e-9) * 0.5"
+Ms_parser(x,y,z) =         "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<1024.e-9) * 8.e5"
+gamma_parser(x,y,z) =      "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<1024.e-9) * -1.759e11"
+exchange_parser(x,y,z) =   "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<1024.e-9) * 1.3e-11"
+anisotropy_parser(x,y,z) = "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<1024.e-9) * -139.26"
+DMI_parser(x,y,z) =        "(x>0.)*(x<1024.e-9)*(y>0.)*(y<1024.e-9)*(z>0.)*(z<1024.e-9) * -4.5e-3"
+
+precession = 1
+demag_coupling = 1
+FFT_solver = 1
+M_normalization = 1  # 0 = unsaturated case; 1 = saturated case
+exchange_coupling = 1
+anisotropy_coupling = 1
+anisotropy_axis = 0.0 0.0 1.0
+DMI_coupling = 1
+
+# INTEGRATION
+
+TimeIntegratorOption = 1 #Forward Euler
+
+integration.type = RungeKutta
+integration.rk.type = 1

Exec/inputs_scaling …c/scaling_inputs/inputs_scaling_gpu_0.25Exec/inputs_scaling renamed to Exec/scaling_inputs/inputs_scaling_gpu_0.25 Exec/inputs_scaling renamed to Exec/scaling_inputs/inputs_scaling_gpu_0.25

@@ -0,0 +1,52 @@
+amrex.use_gpu_aware_mpi=1
+
+n_cell = 256 128 128
+max_grid_size_x = 128
+max_grid_size_y = 128
+max_grid_size_z = 128
+
+dt = 1.e-15
+nsteps = 100
+plot_int = -1
+chk_int = -1
+restart = -1
+
+prob_lo = 0. 0. 0.
+prob_hi = 1024.e-9 512.e-9 512.e-9
+
+mu0 = 1.25663e-6
+
+Mx_parser(x,y,z) = "8.e5 * (x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9)"
+My_parser(x,y,z) = "0."
+Mz_parser(x,y,z) = "0."
+
+# Field 1:  mu_0 Hx=-24.6 mT, mu_0 Hy= 4.3 mT, mu_0 Hz= 0.0 mT
+# which is a field approximately 25 mT, directed 170 degrees counterclockwise from the positive x axis
+timedependent_Hbias = 0
+Hx_bias_parser(x,y,z,t) = "1.e5"
+Hy_bias_parser(x,y,z,t) = "1.e5"
+Hz_bias_parser(x,y,z,t) = "1.e5"
+
+timedependent_alpha = 0
+alpha_parser(x,y,z,t) =    "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 0.5"
+Ms_parser(x,y,z) =         "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 8.e5"
+gamma_parser(x,y,z) =      "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -1.759e11"
+exchange_parser(x,y,z) =   "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * 1.3e-11"
+anisotropy_parser(x,y,z) = "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -139.26"
+DMI_parser(x,y,z) =        "(x>0.)*(x<1024.e-9)*(y>0.)*(y<512.e-9)*(z>0.)*(z<512.e-9) * -4.5e-3"
+
+precession = 1
+demag_coupling = 1
+FFT_solver = 1
+M_normalization = 1  # 0 = unsaturated case; 1 = saturated case
+exchange_coupling = 1
+anisotropy_coupling = 1
+anisotropy_axis = 0.0 0.0 1.0
+DMI_coupling = 1
+
+# INTEGRATION
+
+TimeIntegratorOption = 1 #Forward Euler
+
+integration.type = RungeKutta
+integration.rk.type = 1