mnucci32 / aither Goto Github PK

Issue Type (bug, feature request, other)

Feature request

Description of Issue

Add documentation to Wiki

Issue Type (bug, feature request, other)

Feature request

Description of Issue

Add multi-grid capability to improve convergence.

Hi,
I compiled aither 0.7, 0.8 and 0.9 with mingw64-gcc-7.2.0.
When I used aither 0.8 and 0.9 to run testcase "wallLaw" , it diverged.

aither.exe wallLaw.inp

Aither version 0.9.0

Using MPI Version 2.0
Using 1 process
...
Solution Initialized

Starting wall distance calculation...
Building k-d tree...
K-d tree complete after 0.001 seconds
Wall distance calculation finished after 0.005 seconds

Step NL-Iter CFL Res-Mass Res-Mom-X Res-Mom-Y Res-Mom-Z Res-Energy Res-Tke Res-Omega Max-Eqn Max-Blk Max-I Max-J Max-K Max-Res Res-Matrix
0 0 1.0000e+005 1.0000e+000 1.0000e+000 1.0000e+000 1.0000e+000 1.0000e+000 1.0000e+000 1.0000e+000 7 1 43 0 49 9.7871e-005 4.3013e-006
1 0 1.0000e+005 1.0000e+000 1.0000e+000 1.0000e+000 1.0000e+000 1.0000e+000 2.5130e-001 2.4990e-001 7 1 43 0 49 2.4468e-005 4.1449e-006
2 0 1.0000e+005 1.0000e+000 7.1224e-001 9.6398e-001 1.0000e+000 1.0000e+000 6.8091e-002 6.2386e-002 7 1 43 0 49 6.1172e-006 3.9928e-006
3 0 1.0000e+005 9.8850e-001 3.9045e-001 9.3568e-001 9.9755e-001 9.6239e-001 3.3149e-002 1.5522e-002 7 1 43 0 49 1.5293e-006 3.9684e-006
4 0 1.0000e+005 9.2346e-001 1.9283e-001 8.1248e-001 9.9364e-001 8.8481e-001 3.6305e-002 3.8299e-003 4 1 43 1 0 1.1384e-006 3.9894e-006
5 0 1.0000e+005 9.4928e-001 3.9470e-001 6.6706e-001 9.9185e-001 9.1497e-001 4.1454e-002 9.4175e-004 4 1 43 1 0 1.1356e-006 3.9816e-006
6 0 1.0000e+005 9.5494e-001 4.6842e-001 5.5901e-001 9.8892e-001 9.2872e-001 4.3889e-002 2.3460e-004 4 1 43 1 0 1.1316e-006 3.9248e-006
7 0 1.0000e+005 9.1889e-001 4.2973e-001 4.6601e-001 9.8469e-001 9.0084e-001 4.2301e-002 5.8226e-005 4 1 43 1 0 1.1258e-006 3.8122e-006
8 0 1.0000e+005 8.5154e-001 3.4667e-001 3.7878e-001 9.7976e-001 8.3965e-001 3.9947e-002 1.4301e-005 4 1 43 1 0 1.1204e-006 3.6659e-006
9 0 1.0000e+005 7.7443e-001 2.3396e-001 3.3584e-001 9.7419e-001 7.6777e-001 3.8762e-002 3.5722e-006 4 1 43 1 0 1.1149e-006 3.5319e-006
10 0 1.0000e+005 7.0625e-001 1.5049e-001 3.1234e-001 9.6865e-001 7.0398e-001 3.7521e-002 9.1465e-007 4 1 43 1 0 1.1093e-006 3.4555e-006
11 0 1.0000e+005 6.5928e-001 1.7453e-001 2.8181e-001 9.6338e-001 6.6149e-001 3.6356e-002 4.3135e-007 4 1 43 0 0 1.1038e-006 3.4374e-006
12 0 1.0000e+005 6.4261e-001 2.1936e-001 2.5715e-001 9.5859e-001 6.4645e-001 3.4982e-002 2.9807e-007 4 1 43 0 0 1.0987e-006 3.4386e-006
13 0 1.0000e+005 6.5211e-001 2.1558e-001 2.5682e-001 9.5425e-001 6.5743e-001 3.3547e-002 2.7174e-007 4 1 43 0 0 1.0942e-006 3.4259e-006
14 0 1.0000e+005 6.8016e-001 1.6861e-001 2.7228e-001 9.5019e-001 6.8533e-001 3.2070e-002 2.4710e-007 4 1 43 1 0 1.0896e-006 3.3938e-006
15 0 1.0000e+005 7.1011e-001 1.0676e-001 2.8788e-001 9.4615e-001 7.1627e-001 3.0600e-002 2.3059e-007 4 1 43 1 0 1.0846e-006 3.3534e-006
16 0 1.0000e+005 7.3905e-001 8.0334e-002 2.8828e-001 9.4198e-001 7.4514e-001 2.9167e-002 2.2721e-007 4 1 43 1 0 1.0795e-006 3.3147e-006
17 0 1.0000e+005 7.5547e-001 1.0731e-001 2.7228e-001 9.3750e-001 7.6289e-001 2.7784e-002 2.2705e-007 4 1 43 1 0 1.0740e-006 3.2813e-006
18 0 1.0000e+005 7.5846e-001 1.3338e-001 2.4946e-001 9.3261e-001 7.6603e-001 2.6456e-002 3.4511e-007 4 1 43 1 0 1.0680e-006 3.2586e-006
19 0 1.0000e+005 7.4542e-001 1.3294e-001 2.3004e-001 9.2727e-001 7.5387e-001 2.5184e-002 3.9144e-007 4 1 43 1 0 1.0617e-006 3.2460e-006
20 0 1.0000e+005 7.2167e-001 1.0753e-001 2.1462e-001 9.2162e-001 7.2973e-001 2.3963e-002 2.2378e-007 4 1 43 1 0 1.0553e-006 3.2332e-006
21 0 1.0000e+005 6.9312e-001 7.2727e-002 2.0311e-001 9.1582e-001 7.0168e-001 2.2789e-002 9.2509e+005 4 1 43 1 0 1.0489e-006 5.0983e+003
22 0 1.0000e+005 6.6395e-001 5.4209e-002 3.0390e-001 9.2357e-001 6.7157e-001 1.4645e+008 3.2809e+019 7 1 1 0 1 4.9387e+014 4.5384e+017
23 0 1.0000e+005 6.8313e-001 6.8069e-002 4.6876e-001 1.3394e+000 7.2029e-001 3.7548e+022 5.3049e+046 7 1 17 1 0 1.1533e+043 4.3958e+029
24 0 1.0000e+005 1.1378e+000 6.9496e-002 6.1930e-001 9.4158e-001 1.1525e+000 7.2106e+036 5.8892e+073 7 1 25 1 0 2.4756e+070 1.3644e+033
25 0 1.0000e+005 1.1563e+000 5.1447e-002 6.3364e-001 9.4104e-001 1.1718e+000 1.8027e+036 2.9989e+083 7 1 40 1 0 1.2080e+080 3.4762e+024
26 0 1.0000e+005 1.1585e+000 3.1310e-002 6.4808e-001 9.4103e-001 1.1742e+000 4.5068e+035 7.4975e+082 7 1 40 1 0 3.0201e+079 4.9095e+018
27 0 1.0000e+005 1.1607e+000 2.5005e-002 6.5924e-001 9.4102e-001 1.1769e+000 1.1267e+035 1.8744e+082 7 1 40 1 0 7.5505e+078 2.3099e+015
28 0 1.0000e+005 1.1622e+000 2.8246e-002 6.6737e-001 9.4100e-001 1.1785e+000 2.8169e+034 4.6862e+081 7 1 40 1 0 1.8877e+078 1.5465e+007
29 0 1.0000e+005 1.1635e+000 2.9222e-002 6.7416e-001 9.4099e-001 1.1801e+000 7.0423e+033 1.1716e+081 7 1 40 1 0 4.7193e+077 3.0903e+018
30 0 1.0000e+005 1.1643e+000 2.9030e-002 6.7699e-001 9.4103e-001 1.1809e+000 1.7606e+033 2.9290e+080 7 1 40 1 0 1.1798e+077 4.0000e+020
31 0 1.0000e+005 1.1659e+000 2.7071e-002 6.7778e-001 9.4108e-001 1.1826e+000 4.4016e+032 7.3226e+079 7 1 40 1 0 2.9497e+076 2.6632e+029
32 0 1.0000e+005 1.1644e+000 2.4126e-002 6.8311e-001 9.4102e-001 1.1810e+000 4.9745e+033 1.8307e+079 7 1 40 1 0 7.3744e+075 1.9236e+039
33 0 1.0000e+005 1.1632e+000 1.9522e-002 6.8181e-001 9.4095e-001 1.1799e+000 6.7302e+045 9.9785e+095 7 1 38 1 1 6.1524e+092 2.2847e+048
34 0 1.0000e+005 1.1631e+000 1.5612e-002 6.8524e-001 9.4095e-001 1.1797e+000 3.8707e+055 1.0326e+118 7 1 37 1 2 6.3842e+114 9.5467e+059
35 0 1.0000e+005 1.1650e+000 1.2731e-002 6.7351e-001 9.4096e-001 1.1817e+000 7.2584e+063 4.4387e+136 7 1 36 1 3 2.7449e+133 8.1670e+061
36 0 1.0000e+005 1.1637e+000 1.2200e-002 6.7306e-001 9.4091e-001 1.1804e+000 1.3762e+071 2.5891e+153 7 1 35 1 4 1.6005e+150 1.0880e+066
37 0 1.0000e+005 1.1687e+000 1.1836e-002 6.5227e-001 9.4091e-001 1.1857e+000 3.2421e+076 inf 7 1 34 1 2 1.9387e+159 1.6875e+071
38 0 1.0000e+005 1.1662e+000 1.2774e-002 6.5520e-001 9.4080e-001 1.1832e+000 4.7230e+081 inf 7 1 33 1 2 8.8938e+169 5.4994e+072
39 0 1.0000e+005 1.1692e+000 1.1605e-002 6.5599e-001 9.4089e-001 1.1865e+000 3.2782e+081 inf 7 1 32 1 4 1.1045e+173 2.2026e+085
40 0 1.0000e+005 1.1701e+000 9.5711e-003 6.5959e-001 9.4092e-001 1.1875e+000 4.9896e+086 inf 7 1 31 1 5 5.8543e+185 8.9803e+091
41 0 1.0000e+005 1.1699e+000 9.0252e-003 6.6302e-001 9.4092e-001 1.1875e+000 9.1287e+086 inf 7 1 30 1 6 6.8103e+195 4.7369e+093
42 0 1.0000e+005 1.1713e+000 1.0554e-002 6.5114e-001 9.4091e-001 1.1889e+000 2.4935e+090 inf 7 1 29 1 7 3.9440e+199 7.7202e+093
43 0 1.0000e+005 1.1742e+000 1.2945e-002 6.2504e-001 9.4078e-001 1.1920e+000 2.2346e+090 inf 7 1 28 1 8 2.2063e+200 3.9118e+089
44 0 1.0000e+005 1.1738e+000 1.6261e-002 6.0488e-001 9.4087e-001 1.1915e+000 5.5891e+089 inf 7 1 28 1 8 5.5158e+199 5.8233e+087
45 0 1.0000e+005 1.1735e+000 1.8926e-002 6.0526e-001 9.4338e-001 1.3151e+000 1.3973e+089 inf 7 1 28 1 8 1.3790e+199 9.1242e+085
46 0 1.0000e+005 8.5801e+000 1.8983e-001 1.5742e+001 9.6591e-001 8.8798e+000 3.4934e+088 inf 7 1 28 1 8 3.4475e+198 2.7798e+088
47 0 1.0000e+005 6.7315e+000 3.5800e-001 1.4712e+001 9.5586e-001 6.8583e+000 5.8884e+091 inf 7 1 28 1 8 8.6190e+197 1.3571e+098
48 0 1.0000e+005 6.7857e+000 3.9656e-001 1.8156e+001 9.5619e-001 6.9166e+000 1.6092e+102 inf 7 0 0 0 6 1.0755e+204 1.8845e+085
49 0 1.0000e+005 8.4660e+000 4.2490e-001 2.1498e+001 9.6485e-001 8.6314e+000 4.0232e+101 inf 7 0 0 0 6 2.6889e+203 2.8741e+098
50 0 1.0000e+005 8.4661e+000 4.2489e-001 2.1498e+001 9.6489e-001 8.6315e+000 9.2449e+107 inf 7 0 1 5 12 2.6687e+212 1.6176e+112
51 0 1.0000e+005 8.4662e+000 4.2490e-001 2.1498e+001 9.6493e-001 8.6317e+000 7.5542e+121 inf 7 0 1 5 11 3.1970e+240 2.5116e+124
52 0 1.0000e+005 8.4664e+000 4.2490e-001 2.1498e+001 9.6497e-001 8.6318e+000 8.9802e+137 inf 7 0 1 0 10 1.9606e+268 6.6467e+135
53 0 1.0000e+005 8.4665e+000 4.2491e-001 2.1498e+001 9.6501e-001 8.6320e+000 4.1032e+140 inf 7 0 0 1 10 4.0153e+289 7.1719e+145
54 0 1.0000e+005 8.4667e+000 4.2491e-001 2.1498e+001 9.6506e-001 8.6321e+000 8.4655e+148 inf 7 0 1 4 8 inf nan
Assert failed: nonphysical density
Condition: state_(ii, jj, kk).Rho() > 0
At: aither-0.9.0\src\procBlock.cpp:909

Issue Type (bug, feature request, other)

Feature request

Description of Issue

Add ability to simulate multiple species simultaneously. This is a precursor to reacting flow.

Issue Type (bug, feature request, other)

other

Description of Issue

Could you write up a set of simple steps to visualize the output from one of the sample simulation using Paraview which is able to load Plot3D files, using a simple sample e.g. couette ?

Steps to Reproduce Issue

System Details (OS, compiler, number of processors, etc)

Issue Type (bug, feature request, other)

bug

Description of Issue

linking error with mpi, due to mpi depreciating c++ bindings

Steps to Reproduce Issue

difficult to point out how to reproduce this error on another machine.
mpi 3.1 exists on my machine, and the c++ bindings used in code, were deprecated
cmake file was linking to the mpi c libraries

Solution

i modified the cmake file and linked against the c++ mpi libraries instead of the c mpi libraries, and the executable and shared libraries compiled and linked correctly, but others might face the same issue and don't know how to solve it. might be good if you remove the calls to the c++ bindings, and only use the c bindings.

code section patch :

target_link_libraries (aither ${MPI_CXX_LIBRARIES})
target_link_libraries (aitherStatic ${MPI_CXX_LIBRARIES})
target_link_libraries (aitherShared ${MPI_CXX_LIBRARIES})

System Details (OS, compiler, number of processors, etc)

linux 5.4.0-59-generic on lubuntu 20.04.1 LTS, gcc 9.3.0, mpi 3.1

Issue Type (bug, feature request, other)

Bug

Description of Issue

Simulations that have periodic BCs separated by a single cell, and use a face reconstruction that requires two ghost cells will crash. This should be fixed to help out simulations using multigrid that may coarsen the grid to this state.

Steps to Reproduce Issue

Choose a faceReconstruction like thirdOrder, and run a simulation that uses periodic BCs separated by a single cell.

System Details (OS, compiler, number of processors, etc)

Ubuntu, gcc-8.2, 1

Issue Type (bug, feature request, other)

Feature request

Description of Issue

Add ability to simulate reacting flow for combustion simulations. First multi-species capability must be added