Add a basic TPI sanity test

The floating point exceptions are for now toggled off
in the test body instead of mdrun itself.

Refs #2391

Change-Id: I41b584f4753b9b0e126256a94c1304f0a870aa73

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f5ce6ba11a0246a4e68673f9e12f17b90e774ee1..1c334e0c3f854a56c23da64450bcb227abb08295 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -418,6 +418,7 @@ find_library(HAVE_LIBM m)
 mark_as_advanced(HAVE_LIBM)
 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
 check_library_exists(m feenableexcept "" HAVE_FEENABLEEXCEPT)
+check_library_exists(m fedisableexcept "" HAVE_FEDISABLEEXCEPT)
 
 include(TestSchedAffinity)
 test_sched_affinity(HAVE_SCHED_AFFINITY)

diff --git a/src/config.h.cmakein b/src/config.h.cmakein
index 6059d4821278c3d3c08998d202b356b540dcbfd3..b71a0a4bef4cc4f0a1737baf6b53f28d6b84a145 100644 (file)
--- a/src/config.h.cmakein
+++ b/src/config.h.cmakein
@@ -371,6 +371,9 @@
 /* Define if we have feenableexcept */
 #cmakedefine01 HAVE_FEENABLEEXCEPT
 
+/* Define if we have fedisableexcept */
+#cmakedefine01 HAVE_FEDISABLEEXCEPT
+
 /*! \endcond */
 
 #endif

diff --git a/src/gromacs/math/utilities.cpp b/src/gromacs/math/utilities.cpp
index 7f60d1888fb5a3553af670f72f0793cb2a462722..652f1e603e2656993fef6c41d177b73c94b73ef5 100644 (file)
--- a/src/gromacs/math/utilities.cpp
+++ b/src/gromacs/math/utilities.cpp
@@ -47,10 +47,10 @@
 
 #include <algorithm>
 
-#if !GMX_NATIVE_WINDOWS
-// for fp exception control stuff
-#include <fenv.h>
-#endif
+#include <cfenv>
+
+//! Floating point exception set that we use and care about
+constexpr int c_FPexceptions = FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW;
 
 int
 gmx_within_tol(double   f1,
@@ -120,7 +120,7 @@ int gmx_greatest_common_divisor(int p, int q)
 int gmx_feenableexcept()
 {
 #if HAVE_FEENABLEEXCEPT
-    return feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
+    return feenableexcept(c_FPexceptions);
 #elif (defined(__i386__) || defined(__x86_64__)) && defined(__APPLE__)
     /* Author:  David N. Williams
      * License:  Public Domain
@@ -128,9 +128,8 @@ int gmx_feenableexcept()
      * Might also work on non-Apple Unix. But should be tested
      * before enabling.
      */
-    unsigned int  excepts = FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW;
     static fenv_t fenv;
-    unsigned int  new_excepts = excepts & FE_ALL_EXCEPT;
+    unsigned int  new_excepts = c_FPexceptions & FE_ALL_EXCEPT;
 
     if (fegetenv (&fenv) )
     {
@@ -147,6 +146,28 @@ int gmx_feenableexcept()
 #endif
 }
 
+int gmx_fedisableexcept()
+{
+#if HAVE_FEDISABLEEXCEPT
+    return fedisableexcept(c_FPexceptions);
+#elif (defined(__i386__) || defined(__x86_64__)) && defined(__APPLE__)
+    static fenv_t fenv;
+    unsigned int  new_excepts = c_FPexceptions & FE_ALL_EXCEPT;
+    if (fegetenv (&fenv) )
+    {
+        return -1;
+    }
+
+    // mask
+    fenv.__control |= new_excepts;
+    fenv.__mxcsr   |= new_excepts << 7;
+
+    return fesetenv(&fenv);
+#else
+    return -1;
+#endif
+}
+
 real max_cutoff(real cutoff1, real cutoff2)
 {
     if (cutoff1 == 0 || cutoff2 == 0)

diff --git a/src/gromacs/math/utilities.h b/src/gromacs/math/utilities.h
index eba796a91027c48aaf0ce88b541d1bb282201293..a90cb2b6b55bf1b276f077ecddb9a29cd5e57e92 100644 (file)
--- a/src/gromacs/math/utilities.h
+++ b/src/gromacs/math/utilities.h
@@ -167,6 +167,14 @@ gmx_greatest_common_divisor(int p, int q);
  */
 int gmx_feenableexcept();
 
+/*! \brief Disable floating-point exceptions if supported on OS
+ *
+ * Disables division-by-zero, invalid value, and overflow.
+ *
+ * \returns 0 if successful in disabling exceptions, anything else in case of failure/unsupported OS.
+ */
+int gmx_fedisableexcept();
+
 /*! \brief Return cut-off to use
  *
  * Takes the max of two cut-offs. However a cut-off of 0

diff --git a/src/programs/mdrun/tests/CMakeLists.txt b/src/programs/mdrun/tests/CMakeLists.txt
index c926529a7b85a3076b346ec91a7c6e6aaad67466..7bdc45edef681a9117f2be54d9d514f2c546c646 100644 (file)
--- a/src/programs/mdrun/tests/CMakeLists.txt
+++ b/src/programs/mdrun/tests/CMakeLists.txt
@@ -58,6 +58,7 @@ gmx_add_gtest_executable(
     swapcoords.cpp
     interactiveMD.cpp
     termination.cpp
+    tpitest.cpp
     # pseudo-library for code for testing mdrun
     $<TARGET_OBJECTS:mdrun_test_objlib>
     # pseudo-library for code for mdrun

diff --git a/src/programs/mdrun/tests/refdata/Simple_TpiTest_ReproducesOutput_0.xml b/src/programs/mdrun/tests/refdata/Simple_TpiTest_ReproducesOutput_0.xml
new file mode 100644 (file)
index 0000000..fad2360
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/Simple_TpiTest_ReproducesOutput_0.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Real Name="V">6.4562600000000003</Real>
+  <Real Name="mu">869.80700000000002</Real>
+</ReferenceData>

diff --git a/src/programs/mdrun/tests/refdata/Simple_TpiTest_ReproducesOutput_1.xml b/src/programs/mdrun/tests/refdata/Simple_TpiTest_ReproducesOutput_1.xml
new file mode 100644 (file)
index 0000000..1f20dab
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/Simple_TpiTest_ReproducesOutput_1.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Real Name="V">6.4562600000000003</Real>
+  <Real Name="mu">91.505499999999998</Real>
+</ReferenceData>

diff --git a/src/programs/mdrun/tests/spc216_with_methane.gro b/src/programs/mdrun/tests/spc216_with_methane.gro
new file mode 100644 (file)
index 0000000..7b33f16
--- /dev/null
+++ b/src/programs/mdrun/tests/spc216_with_methane.gro
@@ -0,0 +1,656 @@
+water and methane
+  653
+    1SOL     OW    1   0.005   0.600   0.244  0.1823 -0.4158  0.4875
+    1SOL    HW1    2  -0.017   0.690   0.270 -1.7457 -0.5883 -0.4604
+    1SOL    HW2    3   0.051   0.610   0.161  2.5085 -0.1501  1.7627
+    2SOL     OW    4   0.155   0.341   0.735  0.6282  0.4390  0.0015
+    2SOL    HW1    5   0.140   0.284   0.660 -0.3206  0.0700  0.4631
+    2SOL    HW2    6   0.081   0.402   0.734 -0.1556 -0.4529  1.4404
+    3SOL     OW    7   1.853   0.500   0.554  0.0780  0.6477  0.1596
+    3SOL    HW1    8   1.788   0.505   0.484 -0.5409 -1.2601  0.5636
+    3SOL    HW2    9   1.809   0.533   0.632 -0.0335  0.4430  0.1829
+    4SOL     OW   10   0.732   1.356   1.314  0.3818 -0.1526  0.0053
+    4SOL    HW1   11   0.724   1.291   1.245 -0.6376  0.1642 -0.1766
+    4SOL    HW2   12   0.767   1.434   1.270  0.7292 -0.2888  0.0444
+    5SOL     OW   13   1.746   1.593   0.575 -0.4779 -0.0868  0.0596
+    5SOL    HW1   14   1.735   1.666   0.637  0.2545 -0.2925  0.4446
+    5SOL    HW2   15   1.708   1.518   0.621  1.8857 -0.6672  1.1321
+    6SOL     OW   16   1.759   0.582   0.800  0.1066  0.3638  0.1453
+    6SOL    HW1   17   1.673   0.542   0.815  0.2653 -0.5059 -1.2580
+    6SOL    HW2   18   1.787   0.608   0.888 -0.6999 -1.1652  0.8946
+    7SOL     OW   19   0.965   0.529   0.941  0.0464  0.6791 -0.5470
+    7SOL    HW1   20   0.912   0.531   1.020  0.7588 -0.9814 -0.0074
+    7SOL    HW2   21   0.902   0.533   0.869 -0.5440  3.3012  0.0802
+    8SOL     OW   22   0.091   0.598   1.836  0.0326  0.2995  0.5048
+    8SOL    HW1   23   0.091   0.507   1.806 -1.9591  0.6076 -0.4926
+    8SOL    HW2   24   0.174   0.634   1.804  0.0499 -0.6923 -0.5988
+    9SOL     OW   25   0.796   1.279   0.780  0.0287  0.9120  0.0338
+    9SOL    HW1   26   0.731   1.331   0.734 -0.7066  0.7743  0.9173
+    9SOL    HW2   27   0.799   1.196   0.733  0.1127  1.1975 -0.4621
+   10SOL     OW   28   0.737   0.813   0.145 -0.2045 -0.2755 -0.1129
+   10SOL    HW1   29   0.765   0.723   0.130  2.0853  0.6254 -1.4381
+   10SOL    HW2   30   0.771   0.835   0.231  0.8150 -0.0891 -0.5595
+   11SOL     OW   31   0.547   1.092   0.477  0.7492 -0.2399 -0.7211
+   11SOL    HW1   32   0.529   1.089   0.571 -1.6704 -1.5609 -1.1701
+   11SOL    HW2   33   0.463   1.072   0.436  1.8685 -0.1447 -3.1641
+   12SOL     OW   34   0.729   1.093   1.672 -0.3320 -0.4160 -0.1770
+   12SOL    HW1   35   0.781   1.129   1.744 -3.0691  0.8046  1.2710
+   12SOL    HW2   36   0.762   1.004   1.660 -0.3590 -0.9619  3.2122
+   13SOL     OW   37   0.570   1.373   1.080  0.5042 -0.2319 -0.2229
+   13SOL    HW1   38   0.625   1.297   1.099 -1.3369 -1.5288  0.0461
+   13SOL    HW2   39   0.544   1.361   0.988 -1.9170 -1.3747  0.5551
+   14SOL     OW   40   1.431   1.407   1.448 -0.0622  0.3206 -0.1113
+   14SOL    HW1   41   1.471   1.367   1.526 -0.0250 -0.0867 -0.3344
+   14SOL    HW2   42   1.398   1.332   1.397 -0.3689  0.6034 -0.3325
+   15SOL     OW   43   0.544   0.321   1.628  0.2713  0.2958 -0.0287
+   15SOL    HW1   44   0.458   0.278   1.627  0.2912  0.2480  0.2043
+   15SOL    HW2   45   0.579   0.307   1.540  0.4867 -0.5991  0.1932
+   16SOL     OW   46   1.482   0.418   0.684  0.2029  0.6095 -0.1120
+   16SOL    HW1   47   1.396   0.411   0.641 -0.0022  0.9048  0.2426
+   16SOL    HW2   48   1.490   0.336   0.734 -0.2046  0.9013  0.4457
+   17SOL     OW   49   0.383   1.854   0.680 -0.5139  0.5358  0.4888
+   17SOL    HW1   50   0.421   1.821   0.599  0.7665  0.7680  0.9853
+   17SOL    HW2   51   0.458   1.885   0.731 -1.3106  0.4418  1.7385
+   18SOL     OW   52   1.132   1.589   1.714  0.2895 -0.1975 -0.0185
+   18SOL    HW1   53   1.043   1.553   1.717  0.5306 -0.7027  2.3217
+   18SOL    HW2   54   1.155   1.588   1.621 -0.5281 -4.1539 -0.3015
+   19SOL     OW   55   0.395   1.440   0.467  0.5492  0.0979  0.3540
+   19SOL    HW1   56   0.368   1.353   0.437 -0.1402  0.0430  1.1291
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+   20SOL     OW   58   0.305   1.125   0.948  0.2111 -0.2977 -0.8856
+   20SOL    HW1   59   0.295   1.202   0.892  2.3617  0.9048  0.3267
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+   21SOL     OW   61   0.724   1.826   1.501  0.0298  0.4019 -0.0972
+   21SOL    HW1   62   0.768   1.794   1.579 -0.4863 -1.1317 -0.4356
+   21SOL    HW2   63   0.660   1.759   1.479  0.8721  0.2961 -2.4245
+   22SOL     OW   64   0.514   0.998   0.125  0.6098  0.7181 -0.7434
+   22SOL    HW1   65   0.597   0.957   0.101  0.9105  1.6725 -1.3616
+   22SOL    HW2   66   0.482   1.036   0.043 -0.2917  0.6175 -0.4394
+   23SOL     OW   67   1.315   0.291   1.516 -0.0316  0.1776  0.0042
+   23SOL    HW1   68   1.404   0.271   1.488 -0.3833 -0.6259 -0.5615
+   23SOL    HW2   69   1.300   0.382   1.490 -0.3373 -0.5364 -2.3890
+   24SOL     OW   70   0.062   0.829   0.562 -0.1329 -0.4901  0.1105
+   24SOL    HW1   71   0.100   0.870   0.484 -0.6830 -0.5973 -0.2147
+   24SOL    HW2   72  -0.009   0.888   0.588 -1.4347 -1.6123 -0.8158
+   25SOL     OW   73   0.236   1.600   0.680  0.0347 -0.3240  0.4242
+   25SOL    HW1   74   0.202   1.585   0.592  1.3235 -1.8349  0.1530
+   25SOL    HW2   75   0.267   1.691   0.679 -0.8062 -0.0476 -0.3902
+   26SOL     OW   76   0.071   1.691   0.164  0.0618 -0.1646  0.2129
+   26SOL    HW1   77   0.075   1.759   0.097 -0.3582 -0.6286 -0.2942
+   26SOL    HW2   78   0.089   1.609   0.116  1.2034 -0.3431  0.9259
+   27SOL     OW   79   1.692   0.825   0.708 -0.5641 -0.5462 -0.0453
+   27SOL    HW1   80   1.604   0.794   0.687 -0.6763 -0.2255 -0.0492
+   27SOL    HW2   81   1.733   0.751   0.752 -1.0728 -0.4631  0.5871
+   28SOL     OW   82   1.579   1.053   0.254 -0.8033 -0.0906 -0.0352
+   28SOL    HW1   83   1.484   1.038   0.253 -0.5163 -1.9637 -0.8677
+   28SOL    HW2   84   1.612   0.993   0.321 -0.3926  1.8899  1.5777
+   29SOL     OW   85   0.255   0.444   1.549 -0.3923  0.0985  0.0998
+   29SOL    HW1   86   0.315   0.457   1.623 -0.3069  1.0962 -0.1358
+   29SOL    HW2   87   0.201   0.370   1.575  0.7050 -0.5864  0.4719
+   30SOL     OW   88   0.517   1.454   0.771  0.5258  0.3188  0.1433
+   30SOL    HW1   89   0.540   1.448   0.678 -0.7306  1.1517 -0.2395
+   30SOL    HW2   90   0.432   1.499   0.771 -0.5682 -1.6745  1.5617
+   31SOL     OW   91   1.290   1.247   1.248 -0.1525 -0.1170 -0.3420
+   31SOL    HW1   92   1.225   1.308   1.284  0.8657  0.1540  1.1053
+   31SOL    HW2   93   1.238   1.177   1.208 -1.3298  0.9308 -0.6961
+   32SOL     OW   94   1.161   0.046   0.549 -0.7899  0.0165 -0.2292
+   32SOL    HW1   95   1.234   0.006   0.596 -1.1893 -0.2501  0.1682
+   32SOL    HW2   96   1.172   0.017   0.459 -0.7270 -0.4863 -0.0610
+   33SOL     OW   97   0.200   0.931   1.248  0.1834 -0.0182 -0.3383
+   33SOL    HW1   98   0.256   0.920   1.171  0.0813 -1.0292 -0.2797
+   33SOL    HW2   99   0.213   0.850   1.299 -0.7054  0.0873  0.0770
+   34SOL     OW  100   1.653   0.813   0.403 -0.4229  0.4610 -0.5574
+   34SOL    HW1  101   1.632   0.721   0.384  0.8351  0.2066 -0.7345
+   34SOL    HW2  102   1.697   0.810   0.488 -0.8967  0.9684 -0.2935
+   35SOL     OW  103   1.138   1.632   1.408  0.2235  0.1534 -0.3000
+   35SOL    HW1  104   1.106   1.554   1.363  2.5410 -2.2790  2.0813
+   35SOL    HW2  105   1.080   1.702   1.379 -2.4493 -2.5989 -1.8891
+   36SOL     OW  106   0.309   0.377   1.834 -0.4182 -0.4312 -0.3901
+   36SOL    HW1  107   0.270   0.293   1.810  1.5773 -1.5836  0.2316
+   36SOL    HW2  108   0.356   0.359   1.915 -0.2928  1.3958 -0.0364
+   37SOL     OW  109   1.437   1.245   1.000 -0.0010  0.2071 -0.1808
+   37SOL    HW1  110   1.416   1.156   0.973 -1.6468  1.1111 -1.9656
+   37SOL    HW2  111   1.405   1.252   1.090  0.6670 -1.1529  0.1781
+   38SOL     OW  112   1.424   1.753   0.580  0.2135 -0.3184  0.0506
+   38SOL    HW1  113   1.415   1.709   0.496 -0.3394 -0.8115  0.3676
+   38SOL    HW2  114   1.382   1.694   0.643 -0.0567  0.4046  0.5551
+   39SOL     OW  115   0.842   0.793   0.396 -0.1790 -0.0812 -0.1655
+   39SOL    HW1  116   0.827   0.699   0.405  0.8753 -0.1486  1.0973
+   39SOL    HW2  117   0.773   0.834   0.448 -0.1571 -0.1809 -0.0577
+   40SOL     OW  118   1.184   0.226   0.775  0.0987  0.3445 -0.0968
+   40SOL    HW1  119   1.151   0.212   0.686  1.4235  1.3947 -0.7627
+   40SOL    HW2  120   1.273   0.191   0.774 -0.0295 -0.0600  0.9650
+   41SOL     OW  121   1.645   1.631   0.294 -0.1345  0.2473 -0.0927
+   41SOL    HW1  122   1.700   1.553   0.302  3.4777  2.7807  1.0014
+   41SOL    HW2  123   1.633   1.661   0.384 -2.3958  0.4256 -0.4190
+   42SOL     OW  124   0.990   0.346   1.386  0.0430  0.1267 -0.1927
+   42SOL    HW1  125   1.000   0.372   1.477 -2.1829 -1.0234  0.4135
+   42SOL    HW2  126   1.076   0.311   1.362  1.1511  1.9943  0.9059
+   43SOL     OW  127   1.202   0.168   0.212 -1.0083  0.3755  0.1937
+   43SOL    HW1  128   1.264   0.196   0.145  0.7411 -0.2800  1.5089
+   43SOL    HW2  129   1.128   0.131   0.163  0.1573  0.0522 -1.3518
+   44SOL     OW  130   1.107   1.012   1.474  0.1787 -0.3903  0.2368
+   44SOL    HW1  131   1.103   1.064   1.393 -2.8553 -3.0802 -1.4572
+   44SOL    HW2  132   1.098   1.077   1.544  2.7027  1.9887 -1.5560
+   45SOL     OW  133   1.100   1.061   1.152  0.5007  0.1964  0.5163
+   45SOL    HW1  134   1.055   1.105   1.080  0.6653 -0.2221  0.1570
+   45SOL    HW2  135   1.038   0.995   1.183  0.0876  0.9561  1.3329
+   46SOL     OW  136   1.136   0.703   0.486 -0.1829  0.0543  0.1652
+   46SOL    HW1  137   1.042   0.696   0.470 -0.1004 -2.0729  0.5023
+   46SOL    HW2  138   1.176   0.703   0.399 -0.2869 -2.7402  0.0715
+   47SOL     OW  139   0.205   0.758   0.832  0.1211 -0.5871  0.3969
+   47SOL    HW1  140   0.160   0.782   0.751  0.6567 -1.4270 -0.1532
+   47SOL    HW2  141   0.153   0.798   0.901  0.0933  0.8180 -0.4036
+   48SOL     OW  142   0.014   1.547   1.653  0.0626  0.4351  0.1221
+   48SOL    HW1  143  -0.068   1.593   1.633  0.0169  1.2500  2.0845
+   48SOL    HW2  144  -0.011   1.455   1.659 -0.7796  0.7015  0.9501
+   49SOL     OW  145   0.937   0.550   0.310 -0.4266  0.1699 -0.0318
+   49SOL    HW1  146   0.940   0.460   0.342 -1.3375 -0.2757 -1.1180
+   49SOL    HW2  147   1.018   0.561   0.260 -1.7099 -1.1003 -2.4930
+   50SOL     OW  148   1.594   0.494   1.709 -0.0166  0.2988  0.0705
+   50SOL    HW1  149   1.526   0.554   1.740 -1.2253 -0.8979 -0.2534
+   50SOL    HW2  150   1.597   0.508   1.614  1.3720  1.5596  0.2831
+   51SOL     OW  151   1.317   0.968   0.261 -0.3666  0.0273 -0.2007
+   51SOL    HW1  152   1.326   0.873   0.258  2.6967  0.1307  3.0264
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+   53SOL    HW1  158   1.080   1.291   0.646  0.8360 -1.0279 -3.4337
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+   70SOL    HW1  209   0.592   0.297   0.143  0.6043 -0.4147  1.3207
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+  122SOL    HW2  366   1.892   1.044   1.823 -0.9338  0.2591  0.1444
+  123SOL     OW  367   0.141   1.603   0.414  0.3883  0.0585  0.0978
+  123SOL    HW1  368   0.133   1.634   0.323  0.8960 -0.8732 -0.2699
+  123SOL    HW2  369   0.051   1.606   0.448 -0.0498 -1.0693 -0.9321
+  124SOL     OW  370   1.560   0.559   0.427 -0.0216  0.5022 -0.4211
+  124SOL    HW1  371   1.601   0.486   0.380 -2.0502 -0.9402 -0.0325
+  124SOL    HW2  372   1.511   0.517   0.498 -1.5476  2.2157 -0.4319
+  125SOL     OW  373   0.996   0.813   0.704 -0.1978  0.1388 -0.1498
+  125SOL    HW1  374   1.063   0.744   0.703  0.3067  0.6290 -1.7186
+  125SOL    HW2  375   0.913   0.766   0.693  0.0989 -0.2822 -0.6183
+  126SOL     OW  376   0.868   1.729   1.730  0.0281  0.1797 -0.7823
+  126SOL    HW1  377   0.942   1.789   1.717 -1.1948  1.9851  0.3784
+  126SOL    HW2  378   0.842   1.741   1.821 -0.0835 -2.3569 -0.4305
+  127SOL     OW  379   1.789   1.270   1.671 -0.4728  0.2798  0.3146
+  127SOL    HW1  380   1.723   1.273   1.741 -1.8178  2.0205 -0.9753
+  127SOL    HW2  381   1.770   1.190   1.624  0.7075 -1.1325  2.1509
+  128SOL     OW  382   0.429   1.108   1.723  0.1544 -0.3079  0.1986
+  128SOL    HW1  383   0.516   1.097   1.684 -0.4514  0.4598 -1.4119
+  128SOL    HW2  384   0.368   1.089   1.651 -0.9869  0.7867  0.8568
+  129SOL     OW  385   1.645   0.313   0.302 -0.6779 -0.2001 -0.2455
+  129SOL    HW1  386   1.704   0.328   0.228 -1.1186 -0.2033 -0.5945
+  129SOL    HW2  387   1.596   0.235   0.279 -0.5821 -0.3981  0.2017
+  130SOL     OW  388   0.911   0.913   1.641 -0.9318  0.4624 -0.7830
+  130SOL    HW1  389   0.949   0.979   1.583 -2.1402  1.7456 -0.1606
+  130SOL    HW2  390   0.986   0.867   1.678 -0.0066  2.4026 -0.1816
+  131SOL     OW  391   1.058   1.317   0.952 -0.8086 -0.0363 -0.2081
+  131SOL    HW1  392   1.003   1.272   0.889 -1.2713  0.1838  0.0344
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+  132SOL     OW  394   0.511   1.081   0.739 -1.0025 -0.0666  0.1815
+  132SOL    HW1  395   0.447   1.108   0.805 -2.4376 -1.3233 -0.6516
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+  133SOL    HW1  398   0.233   0.459   0.843  1.5523 -0.2180 -1.5119
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+  135SOL    HW1  404   1.173   0.593   1.479 -0.1192 -1.3540  0.1238
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+  136SOL    HW1  407   1.181   0.176   1.561  1.7731 -1.2568  1.0305
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+  137SOL    HW1  410   0.289   1.413   0.116 -0.5031 -0.3641  0.6618
+  137SOL    HW2  411   0.243   1.432  -0.027  0.0174  1.4375  0.7313
+  138SOL     OW  412   0.105   0.047   0.820  0.3959  0.2991  0.0300
+  138SOL    HW1  413   0.094   0.131   0.776 -0.9519 -0.6603 -1.5166
+  138SOL    HW2  414   0.190   0.015   0.790  0.8202  1.0145  0.4649
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+  140SOL     OW  418   0.964   0.679   1.295  0.2869 -0.2653  0.7807
+  140SOL    HW1  419   0.968   0.634   1.380 -0.0459 -0.5819  0.6255
+  140SOL    HW2  420   0.908   0.624   1.241  1.1585 -0.4952  0.0927
+  141SOL     OW  421   0.038   0.532   1.056  0.4558  0.0500 -0.1209
+  141SOL    HW1  422   0.032   0.488   1.141  1.5562  1.7609  0.8655
+  141SOL    HW2  423   0.123   0.504   1.021  0.3521 -0.0328 -0.3071
+  142SOL     OW  424   0.421   0.753   0.165 -0.0407 -0.2100  0.1967
+  142SOL    HW1  425   0.436   0.844   0.141 -0.5029 -0.0369  0.5633
+  142SOL    HW2  426   0.509   0.717   0.178  0.1348  0.2213  0.2070
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+  143SOL    HW1  428   1.329   0.928   1.716 -1.5403 -0.4747  0.5047
+  143SOL    HW2  429   1.236   0.931   1.596  2.4504  0.6983 -2.6520
+  144SOL     OW  430   0.732   0.704   0.718  0.0771  0.4227  0.0065
+  144SOL    HW1  431   0.709   0.614   0.743  0.0107  0.8290  1.4635
+  144SOL    HW2  432   0.700   0.757   0.790  0.6118  1.5690 -0.5968
+  145SOL     OW  433   1.583   0.679   1.262 -0.3123  0.9622 -0.3549
+  145SOL    HW1  434   1.557   0.609   1.201 -1.5669  1.4574 -0.3935
+  145SOL    HW2  435   1.652   0.639   1.315  0.4282  0.3518 -1.7523
+  146SOL     OW  436   0.528   1.467   1.839  0.3102  0.4490 -0.4735
+  146SOL    HW1  437   0.579   1.460   1.758 -0.3168 -0.4040 -0.8050
+  146SOL    HW2  438   0.442   1.434   1.816  0.4957 -1.0398  0.8606
+  147SOL     OW  439   0.840   0.459   1.175 -0.0390 -0.2074  0.0596
+  147SOL    HW1  440   0.892   0.425   1.247  1.2875  1.0698 -0.2676
+  147SOL    HW2  441   0.758   0.410   1.179  0.2575 -0.5741  2.0556
+  148SOL     OW  442   0.898   1.762   1.289 -0.0258 -0.3272  0.3500
+  148SOL    HW1  443   0.833   1.708   1.245  0.5574 -0.8435  0.1070
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+  149SOL    HW1  446   0.236   0.629   0.414 -0.0976  0.8547  3.1703
+  149SOL    HW2  447   0.156   0.520   0.481  0.2380 -1.5922 -0.2902
+  150SOL     OW  448   0.167   1.257   1.465 -0.0175 -0.1640 -0.2819
+  150SOL    HW1  449   0.226   1.189   1.433  1.2020  1.3149 -1.2321
+  150SOL    HW2  450   0.091   1.209   1.499  2.0974 -2.1736  1.8520
+  151SOL     OW  451   1.448   0.931   1.184  0.1071  0.1399  0.1917
+  151SOL    HW1  452   1.365   0.938   1.232  0.5540  0.1868  0.9605
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+  152SOL     OW  454   1.046   0.926   0.250 -0.6933 -0.1237  0.2538
+  152SOL    HW1  455   1.016   1.015   0.233 -1.1037 -0.7282 -2.3918
+  152SOL    HW2  456   0.981   0.891   0.312 -2.0415  0.5621 -0.7431
+  153SOL     OW  457   1.697   1.681   1.059 -0.2543 -0.7362  0.1995
+  153SOL    HW1  458   1.786   1.691   1.095 -0.3965  0.4371  0.2585
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+  154SOL    HW1  461   1.261   1.758   1.053  1.7480  0.1655  0.5563
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+  156SOL     OW  466   0.413   1.850   0.088  0.6024 -0.0153  0.0548
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+  157SOL    HW1  470   0.692   1.593   0.061 -1.6524  1.2952 -0.2546
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+  158SOL     OW  472   1.458   0.115   0.761  0.6646  0.0012 -0.3672
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+  159SOL     OW  475   1.338   1.663   0.337  0.0918  0.0030 -0.3212
+  159SOL    HW1  476   1.244   1.654   0.324  0.3347  1.1393 -3.3671
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+  160SOL    HW1  479   0.016   0.278   0.110 -1.1478  0.7008  2.8087
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+  161SOL    HW1  482   1.362   0.897   0.559 -0.6926 -1.7377 -1.1492
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+  162SOL    HW1  485   0.812   1.459   1.652  0.5494  0.0827  0.4159
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+  163SOL     OW  487   0.807   1.803   0.428  0.5850  0.0805  0.0023
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+  166SOL    HW1  497  -0.034   0.159   0.535 -1.0624  0.5389  1.8354
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+  193SOL    HW1  578   0.400   0.939   1.457 -0.0335  0.5136 -1.1590
+  193SOL    HW2  579   0.255   0.898   1.478  0.1442  0.7849  0.6396
+  194SOL     OW  580   0.821   1.189   0.033  0.7230  0.2025  0.1811
+  194SOL    HW1  581   0.815   1.128   0.107 -1.5800  0.9849  0.6960
+  194SOL    HW2  582   0.784   1.270   0.067  0.5179  0.8440 -1.5475
+  195SOL     OW  583   0.715   1.616   1.172  0.3272  0.1027  0.1359
+  195SOL    HW1  584   0.756   1.581   1.093  1.3288 -0.8263  1.0564
+  195SOL    HW2  585   0.623   1.628   1.149  0.5732 -0.3826 -1.0964
+  196SOL     OW  586   1.505   1.805   1.833  0.0644 -0.5227 -0.2325
+  196SOL    HW1  587   1.540   1.873   1.775 -0.6363 -0.8056 -0.9864
+  196SOL    HW2  588   1.506   1.846   1.920  0.3753  0.1810 -0.5619
+  197SOL     OW  589   0.838   0.896   1.211 -0.4776 -0.5819  0.4604
+  197SOL    HW1  590   0.751   0.856   1.204 -0.7558  0.0597  0.2601
+  197SOL    HW2  591   0.885   0.839   1.272 -1.7175  0.2815  2.2857
+  198SOL     OW  592   1.331   1.018   0.010 -0.4672 -0.2101 -0.2947
+  198SOL    HW1  593   1.334   0.992   0.102 -1.0490 -0.1719 -0.2637
+  198SOL    HW2  594   1.328   1.113   0.011  1.4277 -0.1154 -0.4045
+  199SOL     OW  595   1.740   1.770   0.797  0.2027  0.2325 -0.0524
+  199SOL    HW1  596   1.736   1.738   0.887  2.6560 -0.4792 -0.1416
+  199SOL    HW2  597   1.811   1.835   0.798 -0.3223  0.8364 -1.2781
+  200SOL     OW  598   0.197   1.145   0.013  0.2240  0.8576  0.7433
+  200SOL    HW1  599   0.278   1.144  -0.037  0.6253  0.5874  1.3956
+  200SOL    HW2  600   0.177   1.238   0.025  0.3334  0.9227  0.4177
+  201SOL     OW  601   0.122   1.292   0.675 -0.3671  0.2154 -0.0378
+  201SOL    HW1  602   0.041   1.320   0.716 -0.5104 -0.4630  0.1516
+  201SOL    HW2  603   0.186   1.359   0.698 -0.4702 -0.0923  1.1957
+  202SOL     OW  604   0.657   1.362   1.581  0.1997 -0.5559 -0.0528
+  202SOL    HW1  605   0.666   1.268   1.596  1.2042 -0.5582 -0.6486
+  202SOL    HW2  606   0.667   1.373   1.486  0.4830  0.1893  0.0563
+  203SOL     OW  607   1.674   0.094   1.271  0.0036 -0.0188  0.0723
+  203SOL    HW1  608   1.766   0.107   1.246 -0.1186  1.3906  0.2757
+  203SOL    HW2  609   1.645   0.018   1.221  0.9219  0.2964 -0.9485
+  204SOL     OW  610   0.406   0.320   0.534 -0.3975  0.8945 -0.0319
+  204SOL    HW1  611   0.332   0.379   0.519 -0.5592 -0.0524 -3.3378
+  204SOL    HW2  612   0.378   0.237   0.494  0.8998 -0.6322  2.1519
+  205SOL     OW  613   1.602   1.329   0.808 -0.0543 -0.2794  0.0018
+  205SOL    HW1  614   1.539   1.298   0.873  0.0647  1.3093  0.8743
+  205SOL    HW2  615   1.685   1.292   0.836 -0.3532 -1.3058 -0.4265
+  206SOL     OW  616   0.504   0.525   1.274 -0.1373  0.6219  0.1464
+  206SOL    HW1  617   0.581   0.508   1.329 -0.1329  1.8063  0.5251
+  206SOL    HW2  618   0.504   0.454   1.210 -0.6928 -1.3916  2.2639
+  207SOL     OW  619   0.939   1.622   0.615  0.0376  0.2169 -0.8057
+  207SOL    HW1  620   0.864   1.660   0.569 -0.2825 -0.9206 -1.2431
+  207SOL    HW2  621   0.946   1.533   0.580  0.4289 -0.3187  0.5869
+  208SOL     OW  622   1.222   0.448   0.958  0.8093  0.1695  0.0716
+  208SOL    HW1  623   1.230   0.403   0.874 -0.7606 -2.3903  1.2470
+  208SOL    HW2  624   1.131   0.478   0.961  0.7570 -0.0912  1.0302
+  209SOL     OW  625   1.162   0.079   1.002 -0.1201  0.0294 -0.0134
+  209SOL    HW1  626   1.152   0.158   0.948 -1.6848 -0.0229  0.1683
+  209SOL    HW2  627   1.090   0.022   0.974  1.8094 -1.9202 -1.1086
+  210SOL     OW  628   0.951   1.274   0.372 -0.2479  0.5020 -0.2795
+  210SOL    HW1  629   1.002   1.247   0.297 -0.3032 -0.8555  0.1568
+  210SOL    HW2  630   1.015   1.296   0.439 -0.2177 -0.1231 -0.1009
+  211SOL     OW  631   0.570   1.596   1.430 -0.0067 -0.0669  0.2383
+  211SOL    HW1  632   0.637   1.550   1.379  0.2717 -0.1940  0.7151
+  211SOL    HW2  633   0.518   1.527   1.471 -1.0547  0.0175 -0.9171
+  212SOL     OW  634   1.490   0.038   0.235  0.3812 -0.5175  0.0030
+  212SOL    HW1  635   1.467  -0.050   0.265  1.2784 -0.8382 -0.2278
+  212SOL    HW2  636   1.472   0.095   0.309  0.9136 -1.0588  0.5495
+  213SOL     OW  637   1.274   0.440   0.514  0.3406 -0.4876 -0.2221
+  213SOL    HW1  638   1.201   0.390   0.477 -0.5303  0.5126  0.1369
+  213SOL    HW2  639   1.247   0.531   0.509  1.3323 -0.1447  0.4304
+  214SOL     OW  640   1.673   0.249   0.968  0.2535  0.0918  0.1841
+  214SOL    HW1  641   1.723   0.211   1.040 -0.3275 -0.9696  0.0332
+  214SOL    HW2  642   1.656   0.339   0.995  0.9016 -0.0077  0.9253
+  215SOL     OW  643   1.625   1.226   0.027  0.6308 -0.1048  0.8494
+  215SOL    HW1  644   1.594   1.313   0.049 -0.0604 -0.0212 -0.4190
+  215SOL    HW2  645   1.593   1.170   0.098  1.5560  0.7563  1.9532
+  216SOL     OW  646   1.002   1.711   0.243  0.1020 -0.6172  0.1515
+  216SOL    HW1  647   0.926   1.677   0.196  0.3933 -1.2573  0.1242
+  216SOL    HW2  648   0.988   1.805   0.248 -2.5080 -1.0870  3.3619
+    1CH4      C  649  -0.024  -0.222  -0.640  0.0000  0.0000  0.0000
+    1CH4     H1  650  -0.083  -0.303  -0.646  0.0000  0.0000  0.0000
+    1CH4     H2  651  -0.080  -0.140  -0.642  0.0000  0.0000  0.0000
+    1CH4     H3  652   0.040  -0.221  -0.716  0.0000  0.0000  0.0000
+    1CH4     H4  653   0.027  -0.225  -0.553  0.0000  0.0000  0.0000
+   1.86206   1.86206   1.86206

diff --git a/src/programs/mdrun/tests/spc216_with_methane.top b/src/programs/mdrun/tests/spc216_with_methane.top
new file mode 100644 (file)
index 0000000..10a8587
--- /dev/null
+++ b/src/programs/mdrun/tests/spc216_with_methane.top
@@ -0,0 +1,33 @@
+#include "oplsaa.ff/forcefield.itp"
+
+[ atomtypes ]
+;name  at.num      mass        charge   ptype       sigma        epsilon
+  CH4    0          0.0        0.000       A        0.371        1.26
+
+#include "oplsaa.ff/spce.itp"
+
+[ moleculetype ]
+; Name            nrexcl
+ methane          3
+
+[ atoms ]
+;   nr       type  resnr residue  atom   cgnr     charge       mass
+     1   opls_138      1    METH     C      1      -0.24     12.011
+     2   opls_140      1    METH    H1      1       0.06      1.008
+     3   opls_140      1    METH    H2      1       0.06      1.008
+     4   opls_140      1    METH    H3      1       0.06      1.008
+     5   opls_140      1    METH    H4      1       0.06      1.008
+
+[ bonds ]
+;  ai    aj funct            c0            c1            c2            c3
+    1     2     1
+    1     3     1
+    1     4     1
+    1     5     1
+
+[ system ]
+Water and methane
+
+[ molecules ]
+SOL     216
+methane   1

diff --git a/src/programs/mdrun/tests/tpitest.cpp b/src/programs/mdrun/tests/tpitest.cpp
new file mode 100644 (file)
index 0000000..afc3198
--- /dev/null
+++ b/src/programs/mdrun/tests/tpitest.cpp
@@ -0,0 +1,153 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * This implements basic TPI sanity test.
+ * It runs the input system with TPI for several steps, and checks the log output.
+ *
+ * \author Aleksei Iupinov <a.yupinov@gmail.com>
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+// FIXME: we should be properly enabling (or, for TPI, disabling) FP exceptions in mdrun, not here.
+// Remove this include and the exception toggling calls.
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textreader.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+#include "moduletest.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+/*! \brief A basic TPI runner.
+ * The only input parameter used currently: input system random seed (ld-seed).
+ */
+class TpiTest : public MdrunTestFixture,
+                public ::testing::WithParamInterface<int>
+{
+    public:
+        //! Runs the test with the given inputs
+        void runTest();
+};
+
+void TpiTest::runTest()
+{
+    runner_.useTopGroAndNdxFromDatabase("spc216_with_methane");
+    runner_.ndxFileName_ = "";
+    ASSERT_EQ(0, runner_.callGrompp());
+
+    gmx_fedisableexcept();
+
+    auto        rerunFileName = fileManager_.getInputFilePath("spc216.gro");
+    CommandLine commandLine;
+    commandLine.append("-rerun");
+    commandLine.append(rerunFileName);
+    ASSERT_EQ(0, runner_.callMdrun(commandLine));
+
+    gmx_feenableexcept();
+
+    const std::string    logFileContexts = TextReader::readFileToString(runner_.logFileName_);
+    const std::string    tpiOutputs      = logFileContexts.substr(logFileContexts.find("Started Test Particle Insertion"));
+
+    TestReferenceData    refData;
+    TestReferenceChecker checker(refData.rootChecker());
+
+    // Output values, their output patterns and relative tolerances (empirical)
+    const std::map<std::string, std::pair<std::string, double> > valuesToCheck = {
+        {"V", {"<V>  =", 1e-10}},
+        {"mu", {"<mu> =", 1e-3}}
+    };
+
+    for (const auto &valueDesc : valuesToCheck)
+    {
+        const auto &name              = valueDesc.first;
+        const auto &pattern           = valueDesc.second.first;
+        const auto &relativeTolerance = valueDesc.second.second;
+        auto        startIndex        = tpiOutputs.find(pattern);
+        ASSERT_NE(startIndex, std::string::npos);
+        startIndex += pattern.size();
+        const double actualValue = std::stod(tpiOutputs.substr(startIndex));
+        checker.setDefaultTolerance(relativeToleranceAsFloatingPoint(actualValue, relativeTolerance));
+        checker.checkDouble(actualValue, name.c_str());
+    }
+}
+
+TEST_P(TpiTest, ReproducesOutput)
+{
+    const int         randomSeed  = GetParam();
+
+    const int         nsteps          = 200;
+    const std::string mdpFileContents = formatString(R"(
+        integrator               = tpi
+        ld-seed                  = %d
+        rtpi                     = 0.05
+        nstlog                   = 0
+        nstenergy                = 0
+        cutoff-scheme            = group
+        nstlist                  = 10
+        ns_type                  = grid
+        rlist                    = 0.9
+        coulombtype              = reaction-field
+        rcoulomb                 = 0.9
+        epsilon-r                = 1
+        epsilon-rf               = 0
+        vdw-type                 = cut-off
+        rvdw                     = 0.9
+        Tcoupl                   = no
+        tc-grps                  = System
+        tau_t                    = 0.5
+        ref_t                    = 298
+        nsteps                   = %d
+    )", randomSeed, nsteps);
+
+    runner_.useStringAsMdpFile(mdpFileContents);
+    runTest();
+}
+
+INSTANTIATE_TEST_CASE_P(Simple, TpiTest, ::testing::Values(1993, 2994));
+
+}
+}
+}