Reading this MSH file fails

[jmeier]

Dear Community,

In Moose I have problems reading the MSH file attached. Because Moose uses libmesh and it looks that the effect is somehow related to libmesh I'd like to ask here for help. The corresponding discussion with Moose can be found here: idaholab/moose#30220

I'm using a FileMeshGenerator in Moose to read the MSH file containing the 8 volumes shown below and want to write it to a .e file:

[Mesh]
  [file]
    type = FileMeshGenerator
    file = "smpl2.msh"
    show_info = true
  []
[]

[Problem]
  solve = false
[]

[Executioner]
  type = Steady
[]

[AuxVariables]
  [dummy]
    order = FIRST
  []
[]

[Outputs]
  exodus = true
[]

The MSH file is a reduced sample from a larger file. This is the smallest file I was able to create showing my problems. Unfortunately, its still very large.

If I import that file, I get 2 (actually 3) problems:

• The names of some of the sidesets are not imported (e.g. srfCD4D). Others are (e.g. srfDE4A) imported.

• One of the node sets gets a negative ID assigned. This leads to the following error message:

  *** ERROR ***
  Your mesh contains nodesets with negative IDs that interfere with QP nodeset IDs potentially generated by the GeometricSearch system.
  

There is one more problem not shown in the file provided below: If the physical name IDs of volumes do not start with 1 but there are lower-dimensional sidesets starting with id=1, the volumes will be ignored (up to my understanding, MSH does not require for each dimension-category to start at 1).

Gmsh is reading the MSH file without problems and shows it correctly.

How can I resolve the problems described above? It is not clear to me, if my MSH file is faulty or there are some issues in libmesh.

The GEO file used

General.AbortOnError = 3;
General.NumThreads = 8;
SetFactory("OpenCASCADE");
Mesh.ElementOrder = 1;
Mesh.CharacteristicLengthFromPoints = 0;
Mesh.CharacteristicLengthFactor = 1;
Geometry.OCCAutoFix = 0;
Point(1) = {-0.00581487501040101, 0.0140383495017886, 0.0299999993294477};
Point(2) = {0, 0.0151949999853969, 0.0299999974668026};
Point(3) = {-0.00387658341787755, 0.00935889966785908, 0.0299999993294477};
Point(4) = {-0.00716299144551158, 0.00716299144551158, 0.0299999993294477};
Point(5) = {-9.70127624067008E-12, 0.0101300003007054, 0.0299999993294477};
Point(6) = {-0.0107444869354367, 0.0107444869354367, 0.0350000001490116};
Point(7) = {-0.0107444869354367, 0.0107444869354367, 0.0299999993294477};
Point(8) = {-0.00387658341787755, 0.00935889966785908, 0.0350000001490116};
Point(9) = {-0.00716299144551158, 0.00716299144551158, 0.0350000001490116};
Point(10) = {-0.0107444869354367, 0.0107444869354367, 0.0249999985098839};
Point(11) = {-0.00716299144551158, 0.00716299144551158, 0.025000000372529};
Point(12) = {-0.00387658341787755, 0.00935889966785908, 0.025000000372529};
Point(13) = {-0.00581487501040101, 0.0140383495017886, 0.0350000001490116};
Point(14) = {-0.0107444869354367, 0.0107444869354367, 0.0399999991059303};
Point(15) = {-0.00581487501040101, 0.0140383495017886, 0.0399999991059303};
Point(16) = {-0.00387658341787755, 0.00935889966785908, 0.0399999991059303};
Point(17) = {-0.00716299144551158, 0.00716299144551158, 0.0399999991059303};
Point(18) = {0, 0.0151949999853969, 0.0349999964237213};
Point(19) = {0, 0.0151949999853969, 0.0399999991059303};
Point(20) = {-9.70127624067008E-12, 0.0101300003007054, 0.0399999991059303};
Point(21) = {0, 0.0101300003007054, 0.0350000001490116};
Point(22) = {-0.00581487501040101, 0.0140383495017886, 0.0199999995529652};
Point(23) = {-0.00581487501040101, 0.0140383495017886, 0.025000000372529};
Point(24) = {-0.00387658341787755, 0.00935889966785908, 0.0199999995529652};
Point(25) = {0, 0.0151949999853969, 0.0249999985098839};
Point(26) = {0, 0.0151949999853969, 0.0199999995529652};
Point(27) = {-9.70127624067008E-12, 0.0101300003007054, 0.0199999995529652};
Point(28) = {0, 0.0101300003007054, 0.025000000372529};
Point(29) = {-0.0140383495017886, 0.00581487501040101, 0.0199999995529652};
Point(30) = {-0.0151949999853969, 0, 0.0199999995529652};
Point(31) = {-0.00935889966785908, 0.0038765836507082, 0.0199999995529652};
Point(32) = {-0.0101300003007054, 3.88051049626803E-11, 0.0199999995529652};
Point(33) = {-0.0107444869354367, 0.0107444869354367, 0.0199999995529652};
Point(34) = {-0.00716299144551158, 0.00716299144551158, 0.0199999995529652};
Point(35) = {-0.0151949999853969, 0, 0.025000000372529};
Point(36) = {-0.0140383495017886, 0.00581487501040101, 0.025000000372529};
Point(37) = {-0.0101300003007054, 3.88051049626803E-11, 0.0299999993294477};
Point(38) = {-0.00935889966785908, 0.0038765836507082, 0.025000000372529};
Point(39) = {-0.0101300003007054, 0, 0.025000000372529};
Point(40) = {-0.0151949999853969, 0, 0.0299999993294477};
Point(41) = {-0.0140383495017886, 0.00581487501040101, 0.0299999993294477};
Point(42) = {-0.00935889966785908, 0.0038765836507082, 0.0299999993294477};
Point(43) = {-0.00935889966785908, 0.0038765836507082, 0.0350000001490116};
Point(44) = {-0.0140383495017886, 0.00581487501040101, 0.0350000001490116};
Point(45) = {-0.0151949999853969, 0, 0.0399999991059303};
Point(46) = {-0.0140383495017886, 0.00581487501040101, 0.0399999991059303};
Point(47) = {-0.0151949999853969, 0, 0.0350000001490116};
Point(48) = {-0.00935889966785908, 0.0038765836507082, 0.0399999991059303};
Point(49) = {-0.0101300003007054, 3.88051049626803E-11, 0.0399999991059303};
Point(50) = {-0.0101300003007054, 0, 0.0350000001490116};
Line(1) = {13, 1};
Line(2) = {1, 7};
Line(3) = {1, 3};
Line(4) = {3, 13};
Line(5) = {1, 6};
Line(6) = {6, 13};
Line(7) = {14, 15};
Line(8) = {15, 13};
Line(9) = {13, 14};
Line(10) = {14, 16};
Line(11) = {15, 16};
Line(12) = {8, 15};
Line(13) = {13, 8};
Line(14) = {7, 6};
Line(15) = {4, 7};
Line(16) = {7, 3};
Line(17) = {9, 6};
Line(18) = {3, 4};
Line(19) = {3, 9};
Line(20) = {9, 8};
Line(21) = {8, 3};
Line(22) = {16, 17};
Line(23) = {8, 17};
Line(24) = {16, 8};
Line(25) = {9, 17};
Line(26) = {1, 2};
Line(27) = {1, 18};
Line(28) = {18, 2};
Line(29) = {13, 18};
Line(30) = {5, 1};
Line(31) = {13, 19};
Line(32) = {19, 18};
Line(33) = {15, 19};
Line(34) = {20, 15};
Line(35) = {18, 20};
Line(36) = {2, 5};
Line(37) = {5, 3};
Line(38) = {3, 21};
Line(39) = {21, 5};
Line(40) = {21, 8};
Line(41) = {2, 21};
Line(42) = {21, 18};
Line(43) = {19, 20};
Line(44) = {20, 16};
Line(45) = {8, 20};
Line(46) = {20, 21};
Line(47) = {29, 35};
Line(48) = {35, 36};
Line(49) = {36, 29};
Line(50) = {29, 30};
Line(51) = {30, 35};
Line(52) = {36, 40};
Line(53) = {40, 41};
Line(54) = {35, 40};
Line(55) = {38, 41};
Line(56) = {39, 40};
Line(57) = {41, 42};
Line(58) = {42, 37};
Line(59) = {37, 41};
Line(60) = {37, 40};
Line(61) = {38, 37};
Line(62) = {42, 38};
Line(63) = {39, 38};
Line(64) = {39, 37};
Line(65) = {31, 32};
Line(66) = {32, 30};
Line(67) = {31, 39};
Line(68) = {32, 39};
Line(69) = {32, 35};
Line(70) = {35, 39};
Line(71) = {29, 31};
Line(72) = {32, 29};
Line(73) = {38, 31};
Line(74) = {31, 36};
Line(75) = {41, 36};
Line(76) = {36, 7};
Line(77) = {7, 10};
Line(78) = {41, 7};
Line(79) = {7, 42};
Line(80) = {10, 4};
Line(81) = {12, 4};
Line(82) = {3, 12};
Line(83) = {29, 10};
Line(84) = {10, 33};
Line(85) = {33, 29};
Line(86) = {36, 10};
Line(87) = {33, 31};
Line(88) = {34, 31};
Line(89) = {31, 11};
Line(90) = {11, 34};
Line(91) = {11, 10};
Line(92) = {36, 38};
Line(93) = {4, 42};
Line(94) = {38, 4};
Line(95) = {4, 11};
Line(96) = {11, 38};
Line(97) = {10, 23};
Line(98) = {22, 33};
Line(99) = {23, 7};
Line(100) = {1, 23};
Line(101) = {12, 1};
Line(102) = {33, 34};
Line(103) = {33, 11};
Line(104) = {24, 34};
Line(105) = {33, 24};
Line(106) = {24, 11};
Line(107) = {12, 24};
Line(108) = {22, 10};
Line(109) = {22, 24};
Line(110) = {11, 12};
Line(111) = {24, 23};
Line(112) = {23, 12};
Line(113) = {23, 22};
Line(114) = {23, 25};
Line(115) = {26, 28};
Line(116) = {28, 25};
Line(117) = {22, 25};
Line(118) = {25, 26};
Line(119) = {26, 22};
Line(120) = {26, 27};
Line(121) = {27, 22};
Line(122) = {27, 24};
Line(123) = {24, 28};
Line(124) = {28, 27};
Line(125) = {28, 12};
Line(126) = {23, 2};
Line(127) = {2, 25};
Line(128) = {12, 5};
Line(129) = {5, 28};
Line(130) = {25, 5};
Line(131) = {6, 14};
Line(132) = {17, 14};
Line(133) = {6, 17};
Line(134) = {44, 14};
Line(135) = {14, 48};
Line(136) = {17, 48};
Line(137) = {43, 17};
Line(138) = {9, 43};
Line(139) = {44, 47};
Line(140) = {41, 47};
Line(141) = {44, 41};
Line(142) = {40, 47};
Line(143) = {42, 50};
Line(144) = {37, 50};
Line(145) = {37, 47};
Line(146) = {46, 44};
Line(147) = {6, 44};
Line(148) = {46, 14};
Line(149) = {48, 46};
Line(150) = {43, 48};
Line(151) = {43, 46};
Line(152) = {44, 43};
Line(153) = {4, 9};
Line(154) = {7, 9};
Line(155) = {41, 6};
Line(156) = {42, 9};
Line(157) = {42, 43};
Line(158) = {42, 44};
Line(159) = {44, 45};
Line(160) = {45, 46};
Line(161) = {47, 45};
Line(162) = {49, 46};
Line(163) = {49, 45};
Line(164) = {50, 45};
Line(165) = {47, 50};
Line(166) = {48, 49};
Line(167) = {43, 49};
Line(168) = {50, 43};
Line(169) = {50, 49};
Physical Curve("linD4A", 1) = {26};
Physical Curve("linD4B", 2) = {-2};
Physical Curve("linD4C", 3) = {78};
Physical Curve("linD4D", 4) = {53};
Curve Loop(1) = {2, 14, -5};
Plane Surface(1) = {1};
Curve Loop(2) = {-16, -2, 3};
Plane Surface(2) = {2};
Curve Loop(3) = {4, 13, 21};
Plane Surface(3) = {3};
Curve Loop(4) = {-3, -1, -4};
Plane Surface(4) = {4};
Curve Loop(5) = {-6, 131, -9};
Plane Surface(5) = {5};
Curve Loop(6) = {-10, 7, 11};
Plane Surface(6) = {6};
Curve Loop(7) = {12, 11, 24};
Plane Surface(7) = {7};
Curve Loop(8) = {-13, -8, -12};
Plane Surface(8) = {8};
Curve Loop(9) = {9, 7, 8};
Plane Surface(9) = {9};
Curve Loop(10) = {22, 132, 10};
Plane Surface(10) = {10};
Curve Loop(11) = {23, -22, 24};
Plane Surface(11) = {11};
Curve Loop(12) = {-20, 25, -23};
Plane Surface(12) = {12};
Curve Loop(13) = {133, -25, 17};
Plane Surface(13) = {13};
Curve Loop(14) = {27, 28, -26};
Plane Surface(14) = {14};
Curve Loop(15) = {-1, 29, -27};
Plane Surface(15) = {15};
Curve Loop(16) = {26, 36, 30};
Plane Surface(16) = {16};
Curve Loop(17) = {-30, 37, -3};
Plane Surface(17) = {17};
Curve Loop(18) = {38, 39, 37};
Plane Surface(18) = {18};
Curve Loop(19) = {-21, -40, -38};
Plane Surface(19) = {19};
Curve Loop(20) = {41, 39, -36};
Plane Surface(20) = {20};
Curve Loop(21) = {-28, -42, -41};
Plane Surface(21) = {21};
Curve Loop(22) = {31, 32, -29};
Plane Surface(22) = {22};
Curve Loop(23) = {-8, 33, -31};
Plane Surface(23) = {23};
Curve Loop(24) = {33, 43, 34};
Plane Surface(24) = {24};
Curve Loop(25) = {-34, 44, -11};
Plane Surface(25) = {25};
Curve Loop(26) = {45, 46, 40};
Plane Surface(26) = {26};
Curve Loop(27) = {-24, -44, -45};
Plane Surface(27) = {27};
Curve Loop(28) = {35, 46, 42};
Plane Surface(28) = {28};
Curve Loop(29) = {-32, 43, -35};
Plane Surface(29) = {29};
Curve Loop(30) = {5, 6, 1};
Plane Surface(30) = {30};
Curve Loop(31) = {19, 20, 21};
Plane Surface(31) = {31};
Curve Loop(32) = {18, 153, -19};
Plane Surface(32) = {32};
Curve Loop(33) = {154, -153, 15};
Plane Surface(33) = {33};
Curve Loop(34) = {14, -17, -154};
Plane Surface(34) = {34};
Curve Loop(35) = {76, 77, -86};
Plane Surface(35) = {35};
Curve Loop(36) = {-75, 78, -76};
Plane Surface(36) = {36};
Curve Loop(37) = {-57, 78, 79};
Plane Surface(37) = {37};
Curve Loop(38) = {-79, -15, 93};
Plane Surface(38) = {38};
Curve Loop(39) = {80, 95, 91};
Plane Surface(39) = {39};
Curve Loop(40) = {-73, -96, -89};
Plane Surface(40) = {40};
Curve Loop(41) = {103, 90, -102};
Plane Surface(41) = {41};
Curve Loop(42) = {-84, -91, -103};
Plane Surface(42) = {42};
Curve Loop(43) = {104, -90, -106};
Plane Surface(43) = {43};
Curve Loop(44) = {18, 15, 16};
Plane Surface(44) = {44};
Curve Loop(45) = {-77, -15, -80};
Plane Surface(45) = {45};
Curve Loop(46) = {99, -2, 100};
Plane Surface(46) = {46};
Curve Loop(47) = {-97, -77, -99};
Plane Surface(47) = {47};
Curve Loop(48) = {81, -18, 82};
Plane Surface(48) = {48};
Curve Loop(49) = {-110, -95, -81};
Plane Surface(49) = {49};
Curve Loop(50) = {101, 3, 82};
Plane Surface(50) = {50};
Curve Loop(51) = {-112, -100, -101};
Plane Surface(51) = {51};
Curve Loop(52) = {108, 97, 113};
Plane Surface(52) = {52};
Curve Loop(53) = {98, -84, -108};
Plane Surface(53) = {53};
Curve Loop(54) = {104, -102, 105};
Plane Surface(54) = {54};
Curve Loop(55) = {-105, -98, 109};
Plane Surface(55) = {55};
Curve Loop(56) = {106, 110, 107};
Plane Surface(56) = {56};
Curve Loop(57) = {117, 118, 119};
Plane Surface(57) = {57};
Curve Loop(58) = {-113, 114, -117};
Plane Surface(58) = {58};
Curve Loop(59) = {126, 127, -114};
Plane Surface(59) = {59};
Curve Loop(60) = {-100, 26, -126};
Plane Surface(60) = {60};
Curve Loop(61) = {128, 129, 125};
Plane Surface(61) = {61};
Curve Loop(62) = {-82, -37, -128};
Plane Surface(62) = {62};
Curve Loop(63) = {130, 129, 116};
Plane Surface(63) = {63};
Curve Loop(64) = {-127, 36, -130};
Plane Surface(64) = {64};
Curve Loop(65) = {111, 112, 107};
Plane Surface(65) = {65};
Curve Loop(66) = {-109, -113, -111};
Plane Surface(66) = {66};
Curve Loop(67) = {-119, 120, 121};
Plane Surface(67) = {67};
Curve Loop(68) = {-121, 122, -109};
Plane Surface(68) = {68};
Curve Loop(69) = {123, 124, 122};
Plane Surface(69) = {69};
Curve Loop(70) = {-107, -125, -123};
Plane Surface(70) = {70};
Curve Loop(71) = {115, 124, -120};
Plane Surface(71) = {71};
Curve Loop(72) = {-118, -116, -115};
Plane Surface(72) = {72};
Curve Loop(73) = {155, -14, -78};
Plane Surface(73) = {73};
Curve Loop(74) = {-141, -147, -155};
Plane Surface(74) = {74};
Curve Loop(75) = {156, -153, 93};
Plane Surface(75) = {75};
Curve Loop(76) = {157, -138, -156};
Plane Surface(76) = {76};
Curve Loop(77) = {158, 152, -157};
Plane Surface(77) = {77};
Curve Loop(78) = {-57, -141, -158};
Plane Surface(78) = {78};
Curve Loop(79) = {47, 48, 49};
Plane Surface(79) = {79};
Curve Loop(80) = {50, 51, -47};
Plane Surface(80) = {80};
Curve Loop(81) = {71, 65, 72};
Plane Surface(81) = {81};
Curve Loop(82) = {-72, 66, -50};
Plane Surface(82) = {82};
Curve Loop(83) = {74, 92, 73};
Plane Surface(83) = {83};
Curve Loop(84) = {52, 53, 75};
Plane Surface(84) = {84};
Curve Loop(85) = {61, -58, 62};
Plane Surface(85) = {85};
Curve Loop(86) = {-63, 64, -61};
Plane Surface(86) = {86};
Curve Loop(87) = {65, 68, -67};
Plane Surface(87) = {87};
Curve Loop(88) = {55, 57, 62};
Plane Surface(88) = {88};
Curve Loop(89) = {-92, -75, -55};
Plane Surface(89) = {89};
Curve Loop(90) = {56, -60, -64};
Plane Surface(90) = {90};
Curve Loop(91) = {-70, 54, -56};
Plane Surface(91) = {91};
Curve Loop(92) = {67, 63, 73};
Plane Surface(92) = {92};
Curve Loop(93) = {-71, -49, -74};
Plane Surface(93) = {93};
Curve Loop(94) = {69, 70, -68};
Plane Surface(94) = {94};
Curve Loop(95) = {66, 51, -69};
Plane Surface(95) = {95};
Curve Loop(96) = {83, 84, 85};
Plane Surface(96) = {96};
Curve Loop(97) = {-49, 86, -83};
Plane Surface(97) = {97};
Curve Loop(98) = {-71, -85, 87};
Plane Surface(98) = {98};
Curve Loop(99) = {-87, 102, 88};
Plane Surface(99) = {99};
Curve Loop(100) = {89, 90, 88};
Plane Surface(100) = {100};
Curve Loop(101) = {-48, 54, -52};
Plane Surface(101) = {101};
Curve Loop(102) = {57, 58, 59};
Plane Surface(102) = {102};
Curve Loop(103) = {-59, 60, 53};
Plane Surface(103) = {103};
Curve Loop(104) = {94, 95, 96};
Plane Surface(104) = {104};
Curve Loop(105) = {-62, -93, -94};
Plane Surface(105) = {105};
Curve Loop(106) = {131, -132, -133};
Plane Surface(106) = {106};
Curve Loop(107) = {134, -131, 147};
Plane Surface(107) = {107};
Curve Loop(108) = {-135, -132, 136};
Plane Surface(108) = {108};
Curve Loop(109) = {137, -25, 138};
Plane Surface(109) = {109};
Curve Loop(110) = {150, -136, -137};
Plane Surface(110) = {110};
Curve Loop(111) = {159, 160, 146};
Plane Surface(111) = {111};
Curve Loop(112) = {139, 161, -159};
Plane Surface(112) = {112};
Curve Loop(113) = {-149, 166, 162};
Plane Surface(113) = {113};
Curve Loop(114) = {-162, 163, 160};
Plane Surface(114) = {114};
Curve Loop(115) = {167, -166, -150};
Plane Surface(115) = {115};
Curve Loop(116) = {164, -163, -169};
Plane Surface(116) = {116};
Curve Loop(117) = {-165, 161, -164};
Plane Surface(117) = {117};
Curve Loop(118) = {-146, 148, -134};
Plane Surface(118) = {118};
Curve Loop(119) = {149, 148, 135};
Plane Surface(119) = {119};
Curve Loop(120) = {151, -149, -150};
Plane Surface(120) = {120};
Curve Loop(121) = {-152, -146, -151};
Plane Surface(121) = {121};
Curve Loop(122) = {140, -139, 141};
Plane Surface(122) = {122};
Curve Loop(123) = {-53, 142, -140};
Plane Surface(123) = {123};
Curve Loop(124) = {143, 168, -157};
Plane Surface(124) = {124};
Curve Loop(125) = {-168, 169, -167};
Plane Surface(125) = {125};
Curve Loop(126) = {58, 144, -143};
Plane Surface(126) = {126};
Curve Loop(127) = {145, 165, -144};
Plane Surface(127) = {127};
Curve Loop(128) = {60, 142, -145};
Plane Surface(128) = {128};
Physical Surface("srfBC4A", 1) = {57, 58};
Physical Surface("srfBC4B", 2) = {52, 53};
Physical Surface("srfBC4C", 3) = {96, 97};
Physical Surface("srfBC4D", 4) = {79, 80};
Physical Surface("srfCD4A", 5) = {59, 60};
Physical Surface("srfCD4B", 6) = {46, 47};
Physical Surface("srfCD4C", 7) = {35, 36};
Physical Surface("srfCD4D", 8) = {84, 101};
Physical Surface("srfDE4A", 9) = {14, 15};
Physical Surface("srfDE4B", 10) = {30, 1};
Physical Surface("srfDE4C", 11) = {73, 74};
Physical Surface("srfDE4D", 12) = {122, 123};
Physical Surface("srfEF4A", 13) = {22, 23};
Physical Surface("srfEF4B", 14) = {9, 5};
Physical Surface("srfEF4C", 15) = {107, 118};
Physical Surface("srfEF4D", 16) = {111, 112};
Surface Loop(1) = {1, 2, 34, 30, 44, 4, 32, 33, 31, 3, 12, 8, 9, 7, 5, 6, 106, 13, 10, 11};
Volume(1) = {1};
Surface Loop(2) = {2, 50, 46, 44, 51, 48, 65, 66, 56, 55, 52, 54, 53, 43, 41, 47, 45, 39, 42, 49};
Volume(2) = {2};
Surface Loop(3) = {3, 19, 8, 4, 18, 26, 17, 20, 16, 14, 15, 21, 22, 23, 29, 24, 25, 7, 27, 28};
Volume(3) = {3};
Surface Loop(4) = {13, 106, 109, 34, 107, 108, 118, 74, 121, 119, 120, 77, 110, 76, 75, 38, 33, 37, 78, 73};
Volume(4) = {4};
Surface Loop(5) = {16, 17, 64, 60, 50, 62, 51, 65, 70, 66, 69, 61, 68, 71, 67, 57, 58, 72, 59, 63};
Volume(5) = {5};
Surface Loop(6) = {35, 36, 45, 97, 89, 37, 88, 83, 105, 104, 38, 40, 39, 100, 99, 41, 98, 93, 96, 42};
Volume(6) = {6};
Surface Loop(7) = {77, 78, 121, 124, 102, 122, 126, 103, 127, 117, 128, 116, 112, 125, 114, 115, 120, 113, 111, 123};
Volume(7) = {7};
Surface Loop(8) = {79, 80, 101, 93, 82, 95, 81, 87, 92, 94, 83, 86, 89, 84, 88, 103, 90, 102, 91, 85};
Volume(8) = {8};
Physical Volume("volBC3A", 1) = {5};
Physical Volume("volBC3B", 2) = {2};
Physical Volume("volBC3C", 3) = {6};
Physical Volume("volBC3D", 4) = {8};
Physical Volume("volCD3A", 5) = {3};
Physical Volume("volCD3B", 6) = {1};
Physical Volume("volCD3C", 7) = {4};
Physical Volume("volCD3D", 8) = {7};
Field[1] = Constant;
Field[1].PointsList = {1,3,4,6,7,8,9,13,14,15,16,17};
Field[1].CurvesList = {1,1,2,2,3,3,4,4,5,5,6,6,7,8,8,9,9,10,10,11,12,12,13,13,14,15,16,16,17,17,18,19,19,20,20,21,22,22,23,23,24,25,25,131,132,132,133,133,153,153,154,154};
Field[1].SurfacesList = {1,2,3,4,5,6,7,8,9,10,11,12,13,30,31,32,33,34,44,106};
Field[1].VolumesList = {1};
Field[1].IncludeBoundary = 0;
Field[1].VIn = 1;
Field[2] = Constant;
Field[2].PointsList = {1,2,3,5,8,13,15,16,18,19,20,21};
Field[2].CurvesList = {1,3,4,4,8,11,11,12,12,13,13,21,21,24,24,26,26,27,27,28,28,29,29,30,30,31,31,32,32,33,34,34,35,35,36,36,37,38,38,39,40,40,41,41,42,42,43,44,44,45,45,46};
Field[2].SurfacesList = {3,4,7,8,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29};
Field[2].VolumesList = {2};
Field[2].IncludeBoundary = 0;
Field[2].VIn = 1;
Field[3] = Constant;
Field[3].PointsList = {29,30,31,32,35,36,37,38,39,40,41,42};
Field[3].CurvesList = {47,47,48,48,49,49,50,50,51,52,52,53,54,55,55,56,56,57,58,58,59,59,60,60,61,61,62,63,63,64,64,65,66,67,67,68,68,69,69,70,70,71,71,72,72,73,74,74,75,75,92,92};
Field[3].SurfacesList = {79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,101,102,103};
Field[3].VolumesList = {3};
Field[3].IncludeBoundary = 0;
Field[3].VIn = 1;
Field[4] = Constant;
Field[4].PointsList = {4,7,10,11,29,31,33,34,36,38,41,42};
Field[4].CurvesList = {15,49,55,55,57,57,62,62,71,73,73,74,74,75,76,76,77,77,78,79,79,80,80,83,83,84,84,85,85,86,86,87,87,88,89,89,90,91,91,92,92,93,93,94,94,95,96,96,102,102,103,103};
Field[4].SurfacesList = {35,36,37,38,39,40,41,42,45,83,88,89,93,96,97,98,99,100,104,105};
Field[4].VolumesList = {4};
Field[4].IncludeBoundary = 0;
Field[4].VIn = 1;
Field[5] = Constant;
Field[5].PointsList = {1,3,4,7,10,11,12,22,23,24,33,34};
Field[5].CurvesList = {2,3,15,15,16,16,18,18,77,80,80,81,81,82,84,90,90,91,91,95,95,97,97,98,98,99,99,100,100,101,101,102,103,103,104,105,105,106,106,107,108,108,109,109,110,110,111,111,112,112,113,113};
Field[5].SurfacesList = {2,39,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,65,66};
Field[5].VolumesList = {5};
Field[5].IncludeBoundary = 0;
Field[5].VIn = 1;
Field[6] = Constant;
Field[6].PointsList = {1,2,3,5,12,22,23,24,25,26,27,28};
Field[6].CurvesList = {3,3,26,30,30,36,37,37,82,82,100,101,101,107,107,109,111,111,112,112,113,114,114,115,115,116,116,117,117,118,118,119,119,120,120,121,121,122,123,123,124,125,125,126,126,127,127,128,128,129,130,130};
Field[6].SurfacesList = {16,17,50,51,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72};
Field[6].VolumesList = {6};
Field[6].IncludeBoundary = 0;
Field[6].VIn = 1;
Field[7] = Constant;
Field[7].PointsList = {4,6,7,9,14,17,41,42,43,44,46,48};
Field[7].CurvesList = {14,14,15,15,17,17,25,57,78,78,79,79,93,131,131,132,133,133,134,134,135,135,136,136,137,137,138,138,141,146,147,147,148,149,149,150,150,151,151,152,152,153,154,154,155,155,156,156,157,157,158,158};
Field[7].SurfacesList = {13,33,34,37,38,73,74,75,76,77,78,106,107,108,109,110,118,119,120,121};
Field[7].VolumesList = {7};
Field[7].IncludeBoundary = 0;
Field[7].VIn = 1;
Field[8] = Constant;
Field[8].PointsList = {37,40,41,42,43,44,45,46,47,48,49,50};
Field[8].CurvesList = {53,53,57,57,58,59,59,60,139,139,140,140,141,141,142,143,143,144,144,145,145,146,146,149,150,151,151,152,152,157,158,158,159,159,160,161,162,162,163,163,164,164,165,165,166,166,167,167,168,168,169,169};
Field[8].SurfacesList = {77,78,102,103,111,112,113,114,115,116,117,120,121,122,123,124,125,126,127,128};
Field[8].VolumesList = {8};
Field[8].IncludeBoundary = 0;
Field[8].VIn = 1;
Field[9] = Min;
Field[9].FieldsList = {1,2,3,4,5,6,7,8};
Background Field = 9;
Printf("{{{***Mesh***}}}");
Mesh.Optimize = 1;
Mesh.OptimizeNetgen = 1;
Mesh.Algorithm3D = 10;
Mesh 3;
Printf("{{{***Mesh***}}}");
Printf("{{{***OptimizeMesh***}}}");
OptimizeMesh "Netgen";
SetOrder 2;
Printf("{{{***OptimizeMesh***}}}");
Printf("{{{***AnalyseMeshQuality***}}}");
Plugin(AnalyseMeshQuality).IGEMeasure = 1;
Plugin(AnalyseMeshQuality).ICNMeasure = 1;
Plugin(AnalyseMeshQuality).DimensionOfElements = -1;
Plugin(AnalyseMeshQuality).Run;
Printf("{{{***AnalyseMeshQuality***}}}");
Printf("Info    : Number of tetrahedra: %g", Mesh.NbTetrahedra);
Mesh.Format = 1;
Save "C:\work\smpl2\.msh";

MSH file smpl2.msh

$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
28
1 1 "linD4A"
1 2 "linD4B"
1 3 "linD4C"
1 4 "linD4D"
2 1 "srfBC4A"
2 2 "srfBC4B"
2 3 "srfBC4C"
2 4 "srfBC4D"
2 5 "srfCD4A"
2 6 "srfCD4B"
2 7 "srfCD4C"
2 8 "srfCD4D"
2 9 "srfDE4A"
2 10 "srfDE4B"
2 11 "srfDE4C"
2 12 "srfDE4D"
2 13 "srfEF4A"
2 14 "srfEF4B"
2 15 "srfEF4C"
2 16 "srfEF4D"
3 1 "volBC3A"
3 2 "volBC3B"
3 3 "volBC3C"
3 4 "volBC3D"
3 5 "volCD3A"
3 6 "volCD3B"
3 7 "volCD3C"
3 8 "volCD3D"
$EndPhysicalNames
$Entities
50 169 128 8
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$EndElements

[roystgnr]

The names of some of the sidesets are not imported (e.g. srfCD4D). Others are (e.g. srfDE4A) imported.

I can replicate this; looking at it now.

One of the node sets gets a negative ID assigned.

And I can replicate this. Looks like there's 3 nodes getting a -2 id.

[roystgnr]

I'm not optimistic about this getting downstream fast (there may be exodiffs in tests which had the same sort of id overlap), but hopefully #4128 fixes the missing sets. If you have a chance to try it out too I'd love feedback. It looks to me like that PR is getting the srf sets from your mesh to show up now ... but I don't see any of the lin sets, which makes me wonder if our GMSH_IO code simply predates our edgeset support. I don't see any add_edge calls in gmsh_io.C.

[roystgnr]

Actually, in addition to any feedback - is there any chance you could generate a smaller .msh with the same set-id overlap problem, so I could add a unit test with it? The smpl2.msh here was perfect for debugging purposes, and I appreciate you cutting it down to that size, but it would still be bigger than any unit test meshes we have in the repo so far.

[jmeier]

Dear @roystgnr

First of all, thank you for putting so much time and effort into this!

I'll try to address the your points in several posts.

On the (negative) physical tag of "Curve 2"
Oh, I missed that the physical tag of this curve in the msh file is negative. In the geo file (used to create the msh file) a positive physical is explicitly given to this entity called "linD4B". This is not the fault of libmesh, of course.
Physical Curve("linD4B", 2) = {-2};

On fixing the import in Moose
I totally understand your point. And it would be great to see the explanation using only the first 13 letters of the alphabet. ;-)

On the collision of the ID's (missing names)
Thanks to your explanation I tried to generate a simple (and smaller) test-case. Please find my first proposal below (this msh file has now 2’944 Bytes). In my (unaltered) version of moose/libmesh the sideset names get overridden by the volume names:

FileMeshGenerator 'file':  Mesh Sidesets:
FileMeshGenerator 'file':   Sideset 1, 2 sides (TRI6), 2 elems (TET10), 9 nodes
FileMeshGenerator 'file':    Side volume: 1
FileMeshGenerator 'file':    Bounding box minimum: (x,y,z)=(-0.333333,        0, -0.333333)
FileMeshGenerator 'file':    Bounding box maximum: (x,y,z)=( 1.33333,        0,  1.33333)
FileMeshGenerator 'file':    Bounding box delta: (x,y,z)=( 1.66667,        0,  1.66667)
FileMeshGenerator 'file':   Sideset 2, 2 sides (TRI6), 2 elems (TET10), 9 nodes
FileMeshGenerator 'file':    Side volume: 1
FileMeshGenerator 'file':    Bounding box minimum: (x,y,z)=(0.666667,        0, -0.333333)
FileMeshGenerator 'file':    Bounding box maximum: (x,y,z)=( 2.33333,        0,  1.33333)
FileMeshGenerator 'file':    Bounding box delta: (x,y,z)=( 1.66667,        0,  1.66667)
FileMeshGenerator 'file': 
FileMeshGenerator 'file':  Mesh Edgesets:
FileMeshGenerator 'file':   None
FileMeshGenerator 'file': 
FileMeshGenerator 'file':  Mesh Subdomains:
FileMeshGenerator 'file':   Subdomain 1 (volBC3A): 3 elems (TET10, 3 active), 18 active nodes
FileMeshGenerator 'file':    Volume: 0.5
FileMeshGenerator 'file':    Bounding box minimum: (x,y,z)=(-0.333333, -0.333333, -0.333333)
FileMeshGenerator 'file':    Bounding box maximum: (x,y,z)=( 1.33333,  1.33333,  1.33333)
FileMeshGenerator 'file':    Bounding box delta: (x,y,z)=( 1.66667,  1.66667,  1.66667)
FileMeshGenerator 'file':   Subdomain 2 (volBC3B): 3 elems (TET10, 3 active), 18 active nodes
FileMeshGenerator 'file':    Volume: 0.5
FileMeshGenerator 'file':    Bounding box minimum: (x,y,z)=(0.666667, -0.333333, -0.333333)
FileMeshGenerator 'file':    Bounding box maximum: (x,y,z)=( 2.33333,  1.33333,  1.33333)
FileMeshGenerator 'file':    Bounding box delta: (x,y,z)=( 1.66667,  1.66667,  1.66667)
FileMeshGenerator 'file':   Global mesh volume = 1

msh-file having ID-collisions

$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
6
1 1 "linD4A"
1 2 "linD4B"
2 1 "srfBC4A"
2 2 "srfBC4B"
3 1 "volBC3A"
3 2 "volBC3B"
$EndPhysicalNames
$Entities
9 21 15 2
1 1 0 1 0
2 2 0 1 0
3 1 0 0 0
4 2 0 0 0
5 2 1 0 0
6 0 0 1 0
7 0 0 0 0
8 0 1 0 0
9 1 1 0 0
1 1.0 0.0 1.0 2.0 0.0 1.0 1 1 2 1 -2
2 1.0 0.0 0.0 1.0 0.0 1.0 0 2 3 -1
3 1.0 0.0 0.0 2.0 0.0 1.0 0 2 3 -2
4 2.0 0.0 0.0 2.0 0.0 1.0 0 2 4 -2
5 1.0 0.0 0.0 2.0 1.0 1.0 0 2 9 -2
6 2.0 0.0 0.0 2.0 1.0 1.0 0 2 5 -2
7 0.0 0.0 1.0 1.0 0.0 1.0 1 2 2 6 -1
8 0.0 0.0 0.0 1.0 0.0 1.0 0 2 3 -6
9 0.0 0.0 0.0 0.0 0.0 1.0 0 2 6 -7
10 0.0 0.0 0.0 1.0 0.0 0.0 0 2 7 -3
11 1.0 0.0 0.0 1.0 1.0 1.0 0 2 9 -1
12 0.0 0.0 0.0 1.0 1.0 1.0 0 2 1 -8
13 0.0 0.0 0.0 0.0 1.0 1.0 0 2 6 -8
14 0.0 1.0 0.0 1.0 1.0 0.0 0 2 8 -9
15 1.0 0.0 0.0 1.0 1.0 0.0 0 2 9 -3
16 0.0 0.0 0.0 1.0 1.0 0.0 0 2 3 -8
17 0.0 0.0 0.0 0.0 1.0 0.0 0 2 7 -8
18 1.0 0.0 0.0 2.0 0.0 0.0 0 2 3 -4
19 1.0 1.0 0.0 2.0 1.0 0.0 0 2 9 -5
20 2.0 0.0 0.0 2.0 1.0 0.0 0 2 5 -4
21 1.0 0.0 0.0 2.0 1.0 0.0 0 2 4 -9
1 0.0 0.0 0.0 1.0 0.0 1.0 1 1 3 8 9 10
2 0.0 0.0 0.0 1.0 0.0 1.0 1 1 3 2 -7 -8
3 1.0 0.0 0.0 2.0 0.0 1.0 1 2 3 3 -1 -2
4 1.0 0.0 0.0 2.0 0.0 1.0 1 2 3 18 4 -3
5 0.0 0.0 0.0 1.0 1.0 0.0 0 3 14 15 16
6 0.0 0.0 0.0 1.0 1.0 0.0 0 3 17 -16 -10
7 0.0 0.0 0.0 1.0 1.0 1.0 0 3 14 11 12
8 0.0 0.0 0.0 1.0 1.0 1.0 0 3 13 -12 -7
9 0.0 0.0 0.0 0.0 1.0 1.0 0 3 -17 -9 13
10 1.0 0.0 0.0 1.0 1.0 1.0 0 3 -2 -15 11
11 1.0 0.0 0.0 2.0 1.0 0.0 0 3 19 20 21
12 1.0 0.0 0.0 2.0 1.0 0.0 0 3 -15 -21 -18
13 1.0 0.0 0.0 2.0 1.0 1.0 0 3 5 -1 -11
14 1.0 0.0 0.0 2.0 1.0 1.0 0 3 6 -5 19
15 2.0 0.0 0.0 2.0 1.0 1.0 0 3 4 -6 20
1 0.0 0.0 0.0 1.0 1.0 1.0 1 1 8 1 2 9 6 10 8 5 7
2 1.0 0.0 0.0 2.0 1.0 1.0 1 2 8 3 4 13 10 12 15 11 14
$EndEntities
$Nodes
36 30 1 31
0 1 0 1
1
1 0 1
0 2 0 1
2
2 0 1
0 3 0 1
3
1 0 0
0 4 0 1
4
2 0 0
0 5 0 1
5
2 1 0
0 6 0 1
6
0 0 1
0 7 0 1
7
0 0 0
0 8 0 1
8
0 1 0
0 9 0 1
9
1 1 0
1 1 0 1
11
1.5 0 1
1 2 0 1
12
1 0 0.5
1 3 0 1
13
1.5 0 0.5
1 4 0 1
14
2 0 0.5
1 5 0 1
15
1.5 0.5 0.5
1 6 0 1
16
2 0.5 0.5
1 7 0 1
17
0.5 0 1
1 8 0 1
18
0.5 0 0.5
1 9 0 1
19
0 0 0.5
1 10 0 1
20
0.5 0 0
1 11 0 1
21
1 0.5 0.5
1 12 0 1
22
0.5 0.5 0.5
1 13 0 1
23
0 0.5 0.5
1 14 0 1
24
0.5 1 0
1 15 0 1
25
1 0.5 0
1 16 0 1
26
0.5 0.5 0
1 17 0 1
27
0 0.5 0
1 18 0 1
28
1.5 0 0
1 19 0 1
29
1.5 1 0
1 20 0 1
30
2 0.5 0
1 21 0 1
31
1.5 0.5 0
2 1 0 0
2 2 0 0
2 3 0 0
2 4 0 0
3 1 0 0
3 2 0 0
$EndNodes
$Elements
8 12 94 135
1 1 8 1
94 1 2 11
1 7 8 1
100 6 1 17
2 1 9 1
115 3 6 7 18 19 20
2 2 9 1
116 1 6 3 17 18 12
2 3 9 1
117 1 3 2 12 13 11
2 4 9 1
118 2 3 4 13 28 14
3 1 11 3
130 6 3 7 8 18 20 19 23 27 26
131 9 8 3 1 24 26 25 21 12 22
132 6 3 8 1 18 26 23 17 22 12
3 2 11 3
133 3 2 9 1 13 15 25 12 21 11
134 2 4 9 5 14 31 15 16 29 30
135 2 3 9 4 13 25 15 14 31 28
$EndElements

geo-file for generating the msh-file having ID-collisions

General.AbortOnError = 3;
General.NumThreads = 8;
SetFactory("OpenCASCADE");
Mesh.ElementOrder = 1;
Mesh.CharacteristicLengthFromPoints = 0;
Mesh.CharacteristicLengthFactor = 10;
Geometry.OCCAutoFix = 0;
Point(1) = {1, 0, 1};
Point(2) = {2, 0, 1};
Point(3) = {1, 0, 0};
Point(4) = {2, 0, 0};
Point(5) = {2, 1, 0};
Point(6) = {0, 0, 1};
Point(7) = {0, 0, 0};
Point(8) = {0, 1, 0};
Point(9) = {1, 1, 0};
Line(1) = {1, 2};
Line(2) = {3, 1};
Line(3) = {3, 2};
Line(4) = {4, 2};
Line(5) = {9, 2};
Line(6) = {5, 2};
Line(7) = {6, 1};
Line(8) = {3, 6};
Line(9) = {6, 7};
Line(10) = {7, 3};
Line(11) = {9, 1};
Line(12) = {1, 8};
Line(13) = {6, 8};
Line(14) = {8, 9};
Line(15) = {9, 3};
Line(16) = {3, 8};
Line(17) = {7, 8};
Line(18) = {3, 4};
Line(19) = {9, 5};
Line(20) = {5, 4};
Line(21) = {4, 9};
Physical Curve("linD4A", 1) = {1};
Physical Curve("linD4B", 2) = {7};
Curve Loop(1) = {8, 9, 10};
Plane Surface(1) = {1};
Curve Loop(2) = {2, -7, -8};
Plane Surface(2) = {2};
Curve Loop(3) = {3, -1, -2};
Plane Surface(3) = {3};
Curve Loop(4) = {18, 4, -3};
Plane Surface(4) = {4};
Curve Loop(5) = {14, 15, 16};
Plane Surface(5) = {5};
Curve Loop(6) = {-16, -10, 17};
Plane Surface(6) = {6};
Curve Loop(7) = {14, 11, 12};
Plane Surface(7) = {7};
Curve Loop(8) = {-12, -7, 13};
Plane Surface(8) = {8};
Curve Loop(9) = {-9, 13, -17};
Plane Surface(9) = {9};
Curve Loop(10) = {-15, 11, -2};
Plane Surface(10) = {10};
Curve Loop(11) = {19, 20, 21};
Plane Surface(11) = {11};
Curve Loop(12) = {-21, -18, -15};
Plane Surface(12) = {12};
Curve Loop(13) = {-1, -11, 5};
Plane Surface(13) = {13};
Curve Loop(14) = {-5, 19, 6};
Plane Surface(14) = {14};
Curve Loop(15) = {4, -6, 20};
Plane Surface(15) = {15};
Physical Surface("srfBC4A", 1) = {1, 2};
Physical Surface("srfBC4B", 2) = {3, 4};
Surface Loop(1) = {1, 2, 9, 6, 10, 8, 5, 7};
Volume(1) = {1};
Surface Loop(2) = {3, 4, 13, 10, 12, 15, 11, 14};
Volume(2) = {2};
Physical Volume("volBC3A", 1) = {1};
Physical Volume("volBC3B", 2) = {2};
Field[1] = Constant;
Field[1].PointsList = {1,3,6,7,8,9};
Field[1].CurvesList = {2,2,7,8,8,9,9,10,10,11,12,12,13,14,15,15,16,16,17,17};
Field[1].SurfacesList = {1,2,5,6,7,8,9,10};
Field[1].VolumesList = {1};
Field[1].IncludeBoundary = 0;
Field[1].VIn = 1;
Field[2] = Constant;
Field[2].PointsList = {1,2,3,4,5,9};
Field[2].CurvesList = {1,2,3,3,4,5,5,6,6,11,11,15,18,18,19,20,21,21};
Field[2].SurfacesList = {3,4,10,11,12,13,14,15};
Field[2].VolumesList = {2};
Field[2].IncludeBoundary = 0;
Field[2].VIn = 1;
Field[3] = Min;
Field[3].FieldsList = {1,2};
Background Field = 3;
Mesh.Optimize = 1;
Mesh.OptimizeNetgen = 1;
Mesh.Algorithm3D = 10;
Mesh 3;
OptimizeMesh "Netgen";
SetOrder 2;
Mesh.Format = 1;
Save "C:\work\id-coll.msh";
Exit 0;

Testing
I'll try that later today.

Again, thanks for your time and your support!

[jmeier]

Dear @roystgnr,

I created an issue over there with gmsh: As it turns out, the negative ID denotes the orientation of the entity. Citing from the issue with gmsh:

In the MSH4 file format, the sign of the physical tag in the $Entities field encode the orientation of the entity that is part of the physical group (in your case it comes from the fact that you defined the physical group 2 as made up of line -2)

Would it be possible in libmesh to use the absolute of the physical ID and to reverse the order of the nodes if the id is negative?

[roystgnr]

What an odd encoding. I would have stored "foo bar 2" as "foo bar 2" rather than "bar foo -2", myself.

Their alternative is at least well-defined for line elements, where the 2-element symmetry group is isomorphic to <{1,-1},×>, but is there an interpretation for other element types as well? The symmetry group of a triangle has 6 elements, 3 of which are of the opposite orientation to the identity and the other two. If we see a negative there, which of those three flips do we use? Keep the first node as the first node, I guess? The docs at https://gmsh.info/doc/texinfo/gmsh.html say that negative tags have this "reverse orientation" interpretation for surfaces as well as curves, but don't get any more specific.

Thanks for the new mesh; I've added it to a unit test in my PR and hope to merge it and the fix it tests into libMesh master shortly.