Remove unnecessary includes of arrayref.h

Changed to forward declaration.
Don't think I got all of them yet.

Change-Id: I7c148364db152ed0a6645e91ee1ab93421441c0d

diff --git a/src/gromacs/analysisdata/framelocaldata.h b/src/gromacs/analysisdata/framelocaldata.h
index 432926cbc89151b032e7b50746575cf09b653221..33d9e977ed0f93c93adc7778fa28350c1dcfb9c9 100644 (file)
--- a/src/gromacs/analysisdata/framelocaldata.h
+++ b/src/gromacs/analysisdata/framelocaldata.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2019,2020, 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.
@@ -47,12 +47,14 @@
 #include <vector>
 
 #include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
+
 //! \addtogroup module_analysisdata
 //! \{
 

diff --git a/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp b/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
index 3b7343b717bace01e34a57a0fe5a39aceb94efae..27be15efb38e7f7ea9c0517d5a30add61bed8372 100644 (file)
--- a/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
+++ b/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -47,6 +47,7 @@
 #include <vector>
 
 #include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/utility/arrayref.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/applied_forces/densityfittingamplitudelookup.h b/src/gromacs/applied_forces/densityfittingamplitudelookup.h
index 9b32472cf56bca2cd9d4c7f6b19c1f4f5b1f7e96..86675bcec649c882f9021e06867e2d569bcd3561 100644 (file)
--- a/src/gromacs/applied_forces/densityfittingamplitudelookup.h
+++ b/src/gromacs/applied_forces/densityfittingamplitudelookup.h
@@ -44,8 +44,8 @@
 
 #include <map>
 #include <memory>
+#include <vector>
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/enumerationhelpers.h"
 #include "gromacs/utility/real.h"
 
@@ -54,6 +54,9 @@ struct t_mdatoms;
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
+
 /*! \brief
  * The methods that determine how amplitudes are spread on a grid in density guided simulations.
  */

diff --git a/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp b/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
index 531052885e601b47ad30d8e31a8c3c7239396d6f..2cd5125bfcc56220a0b90e03dc2ad7f978cb19d4 100644 (file)
--- a/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
+++ b/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -48,6 +48,7 @@
 #include <gtest/gtest.h>
 
 #include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/utility/arrayref.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/awh/biasstate.h b/src/gromacs/awh/biasstate.h
index 161a4bd1eea044638c9a496c5098e22424a4b746..b36c5e86e8c17fe1299c522f50aa6f5435ef1aa0 100644 (file)
--- a/src/gromacs/awh/biasstate.h
+++ b/src/gromacs/awh/biasstate.h
@@ -58,7 +58,6 @@
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/alignedallocator.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/gmxassert.h"
 
@@ -72,6 +71,8 @@ struct t_commrec;
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
 struct AwhBiasHistory;
 struct AwhBiasParams;
 class BiasParams;

diff --git a/src/gromacs/awh/coordstate.h b/src/gromacs/awh/coordstate.h
index e3d2550cabb5c551535061009d653d4da2de8004..f924ef449d592156fcbb9a17e4eb58007d344867 100644 (file)
--- a/src/gromacs/awh/coordstate.h
+++ b/src/gromacs/awh/coordstate.h
@@ -54,13 +54,13 @@
 
 #include <vector>
 
-#include "gromacs/utility/arrayref.h"
-
 #include "dimparams.h"
 
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
 struct AwhBiasParams;
 struct AwhBiasStateHistory;
 class BiasParams;

diff --git a/src/gromacs/awh/correlationgrid.h b/src/gromacs/awh/correlationgrid.h
index 742d760ca2bd064e95df4eff3c61aaed34eba9a2..a1c4338d039954adee0fdc36736efb97153f8e26 100644 (file)
--- a/src/gromacs/awh/correlationgrid.h
+++ b/src/gromacs/awh/correlationgrid.h
@@ -50,7 +50,6 @@
 
 #include <vector>
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/gmxassert.h"
 
@@ -59,6 +58,8 @@
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
 struct CorrelationGridHistory;
 
 /*! \internal

diff --git a/src/gromacs/awh/histogramsize.cpp b/src/gromacs/awh/histogramsize.cpp
index f405685d747556a41aebc61714a0ab478130aa04..fcfd452d4a2e441553f9f6ab983c484566305ce3 100644 (file)
--- a/src/gromacs/awh/histogramsize.cpp
+++ b/src/gromacs/awh/histogramsize.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, 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.
@@ -54,6 +54,7 @@
 
 #include "gromacs/mdtypes/awh_history.h"
 #include "gromacs/mdtypes/awh_params.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 

diff --git a/src/gromacs/awh/histogramsize.h b/src/gromacs/awh/histogramsize.h
index 7fb3a21ce9c6b663c9b7dd81ca4425930c217472..7d9313549cd8443ec0e042e722e1785c25b9c94f 100644 (file)
--- a/src/gromacs/awh/histogramsize.h
+++ b/src/gromacs/awh/histogramsize.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, 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.
@@ -57,11 +57,12 @@
 #include <vector>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
 struct AwhBiasStateHistory;
 struct AwhBiasParams;
 class BiasParams;

diff --git a/src/gromacs/awh/tests/biasstate.cpp b/src/gromacs/awh/tests/biasstate.cpp
index dcf43a9f662007ecc5225b8852cf99b67b5c874d..cdb08acd00afef27380f8b1fd42289ed7081c35f 100644 (file)
--- a/src/gromacs/awh/tests/biasstate.cpp
+++ b/src/gromacs/awh/tests/biasstate.cpp
@@ -48,6 +48,7 @@
 #include "gromacs/awh/pointstate.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/mdtypes/awh_params.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/commandline/filenm.cpp b/src/gromacs/commandline/filenm.cpp
index 696368f08a7f2e5f09587362f82da8a254e4b439..ec798075f3f6056d8ad6241d3712141569df5fad 100644 (file)
--- a/src/gromacs/commandline/filenm.cpp
+++ b/src/gromacs/commandline/filenm.cpp
@@ -46,6 +46,7 @@
 #include <string_view>
 
 #include "gromacs/fileio/filetypes.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/commandline/filenm.h b/src/gromacs/commandline/filenm.h
index d5e654abb076690e643f582ae1fd2afe299735e3..5cc0e620a15b1781a7f0962311abea25de300f70 100644 (file)
--- a/src/gromacs/commandline/filenm.h
+++ b/src/gromacs/commandline/filenm.h
@@ -50,13 +50,18 @@
 #include <vector>
 
 #include "gromacs/fileio/filetypes.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 
 
 //! \addtogroup module_commandline
 //! \{
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+} // namespace gmx
+
 /*! \brief
  * File name option definition for C code.
  *

diff --git a/src/gromacs/coordinateio/tests/requirements.h b/src/gromacs/coordinateio/tests/requirements.h
index 9afbfbf243e4bd81465d3c6487335f9ac680260a..8a91f71262eea677e90be24eeb09b799a88db565 100644 (file)
--- a/src/gromacs/coordinateio/tests/requirements.h
+++ b/src/gromacs/coordinateio/tests/requirements.h
@@ -52,7 +52,6 @@
 #include "gromacs/coordinateio/requirements.h"
 #include "gromacs/options/options.h"
 #include "gromacs/utility/any.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "gromacs/coordinateio/tests/coordinate_test.h"
@@ -60,6 +59,9 @@
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
+
 namespace test
 {
 

diff --git a/src/gromacs/domdec/box.h b/src/gromacs/domdec/box.h
index d02c34b9d802799ea750f17f943b89ce4bf2ad87..4cc482b4021324192e81990fbcf49b4fd92d56e4 100644 (file)
--- a/src/gromacs/domdec/box.h
+++ b/src/gromacs/domdec/box.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, 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.
@@ -47,8 +47,12 @@
 #include <vector>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
 struct gmx_ddbox_t;
 struct gmx_domdec_t;
 struct t_commrec;

diff --git a/src/gromacs/domdec/cellsizes.h b/src/gromacs/domdec/cellsizes.h
index d35da8357f9421f2fabf4e16415db47ea5a070ed..cf07585e89c62133cae9a41c677865a55608d826 100644 (file)
--- a/src/gromacs/domdec/cellsizes.h
+++ b/src/gromacs/domdec/cellsizes.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, 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.
@@ -47,8 +47,12 @@
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/arrayref.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
 struct gmx_ddbox_t;
 struct gmx_domdec_comm_t;
 struct gmx_domdec_t;

diff --git a/src/gromacs/domdec/collect.h b/src/gromacs/domdec/collect.h
index 4d4b3b766f912f1b4331973f6ff42f0e59d8ba8f..62d28c0f2a7571b8edefae4aae4be156ba55ad2f 100644 (file)
--- a/src/gromacs/domdec/collect.h
+++ b/src/gromacs/domdec/collect.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, 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.
@@ -44,8 +44,12 @@
 #define GMX_DOMDEC_COLLECT_H
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
 struct gmx_domdec_t;
 class t_state;
 

diff --git a/src/gromacs/domdec/domdec_network.h b/src/gromacs/domdec/domdec_network.h
index 902dbb768ad1a7505812554bc733f516e5af8d14..48d8702bcd5b444b3ad7f66f13571c5818ef0676 100644 (file)
--- a/src/gromacs/domdec/domdec_network.h
+++ b/src/gromacs/domdec/domdec_network.h
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 2008-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -50,10 +50,14 @@
 #define GMX_DOMDEC_DOMDEC_NETWORK_H
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 
 struct gmx_domdec_t;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
 /* \brief */
 enum
 {

diff --git a/src/gromacs/domdec/localatomset.h b/src/gromacs/domdec/localatomset.h
index 594c18b5c2169f1028c704d4d728d096ac9e686d..41599d37b21790c550095888e307a09a1acfa4ed 100644 (file)
--- a/src/gromacs/domdec/localatomset.h
+++ b/src/gromacs/domdec/localatomset.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, 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.
@@ -43,11 +43,12 @@
 #ifndef GMX_DOMDEC_LOCALATOMSET_H
 #define GMX_DOMDEC_LOCALATOMSET_H
 
-#include "gromacs/utility/arrayref.h"
+#include <cstddef>
 
 namespace gmx
 {
-
+template<typename>
+class ArrayRef;
 namespace internal
 {
 class LocalAtomSetData;

diff --git a/src/gromacs/domdec/localatomsetmanager.h b/src/gromacs/domdec/localatomsetmanager.h
index 2c7bafed200b71ff6b00770d4248946162829db9..8a2c227f32bd2ec65b53e03f5a4d4a9ce0a73bd8 100644 (file)
--- a/src/gromacs/domdec/localatomsetmanager.h
+++ b/src/gromacs/domdec/localatomsetmanager.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, 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.
@@ -46,7 +46,6 @@
 
 #include <memory>
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/classhelpers.h"
 
@@ -54,7 +53,8 @@ class gmx_ga2la_t;
 
 namespace gmx
 {
-
+template<typename>
+class ArrayRef;
 class LocalAtomSet;
 
 /*! \libinternal \brief

diff --git a/src/gromacs/domdec/tests/localatomsetmanager.cpp b/src/gromacs/domdec/tests/localatomsetmanager.cpp
index 282ad6824e957d54ba0b130270de25a336da423b..6feb1b03d3dbb94e0b28f6a8f42a039cbafbe0e6 100644 (file)
--- a/src/gromacs/domdec/tests/localatomsetmanager.cpp
+++ b/src/gromacs/domdec/tests/localatomsetmanager.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, 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.
@@ -51,6 +51,7 @@
 #include <gtest/gtest.h>
 
 #include "gromacs/domdec/localatomset.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/exceptions.h"
 
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/domdec/utility.h b/src/gromacs/domdec/utility.h
index 89e804aaf62d69c18bfde9de9b23f51427b0d4bc..e3fea6e1e7de42a3a8ac38732011c4b80fa77800 100644 (file)
--- a/src/gromacs/domdec/utility.h
+++ b/src/gromacs/domdec/utility.h
@@ -44,10 +44,15 @@
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdtypes/forcerec.h"
-#include "gromacs/utility/arrayref.h"
 
 #include "domdec_internal.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /*! \brief Returns true if the DLB state indicates that the balancer is on. */
 static inline bool isDlbOn(const gmx_domdec_comm_t* comm)
 {

diff --git a/src/gromacs/ewald/pme.h b/src/gromacs/ewald/pme.h
index 11fe0873893f49c4aced6c073d81827cdbbfa297..d60f2e6326150c03dfbc6a145356535767b086ac 100644 (file)
--- a/src/gromacs/ewald/pme.h
+++ b/src/gromacs/ewald/pme.h
@@ -54,7 +54,6 @@
 #include "gromacs/gpu_utils/devicebuffer_datatype.h"
 #include "gromacs/gpu_utils/gpu_macros.h"
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
@@ -78,6 +77,8 @@ class GpuEventSynchronizer;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class ForceWithVirial;
 class MDLogger;
 enum class PinningPolicy : int;

diff --git a/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.h b/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.h
index e1186a2f3abf711aa1feea710b2ffda0c1dc1325..9094a7c7b3483cdc64744ce13f2e150506b7f073 100644 (file)
--- a/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.h
+++ b/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.h
@@ -43,6 +43,8 @@
 #ifndef GMX_PMECOORDINATERECEIVERGPU_IMPL_H
 #define GMX_PMECOORDINATERECEIVERGPU_IMPL_H
 
+#include <vector>
+
 #include "gromacs/ewald/pme_coordinate_receiver_gpu.h"
 #include "gromacs/utility/arrayref.h"
 
@@ -50,7 +52,6 @@ class GpuEventSynchronizer;
 
 namespace gmx
 {
-
 /*! \internal \brief Class with interfaces and data for CUDA version of PME coordinate receiving functionality */
 
 class PmeCoordinateReceiverGpu::Impl

diff --git a/src/gromacs/ewald/pme_gpu_internal.h b/src/gromacs/ewald/pme_gpu_internal.h
index 9a15c3bbc986f0b0141a84dc61db2ac1fd11f3cf..f2cbc94c5dbbffbd35ffd6843db6e752b65cee15 100644 (file)
--- a/src/gromacs/ewald/pme_gpu_internal.h
+++ b/src/gromacs/ewald/pme_gpu_internal.h
@@ -49,7 +49,6 @@
 #include "gromacs/fft/fft.h" // for the gmx_fft_direction enum
 #include "gromacs/gpu_utils/devicebuffer_datatype.h"
 #include "gromacs/gpu_utils/gpu_macros.h" // for the GPU_FUNC_ macros
-#include "gromacs/utility/arrayref.h"
 
 #include "pme_gpu_types_host.h"
 #include "pme_output.h"
@@ -72,6 +71,8 @@ struct t_complex;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class MDLogger;
 } // namespace gmx
 

diff --git a/src/gromacs/ewald/tests/pmetestcommon.h b/src/gromacs/ewald/tests/pmetestcommon.h
index 7f2e727c5f302ec2c9ac8185f71f050877627349..8e6e135409cba986af20d6f81c8325dbd37ba011 100644 (file)
--- a/src/gromacs/ewald/tests/pmetestcommon.h
+++ b/src/gromacs/ewald/tests/pmetestcommon.h
@@ -50,13 +50,15 @@
 #include "gromacs/ewald/pme_gpu_internal.h"
 #include "gromacs/math/gmxcomplex.h"
 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/unique_cptr.h"
 
 namespace gmx
 {
 
 class DeviceStreamManager;
+template<typename>
+class ArrayRef;
+
 namespace test
 {
 

diff --git a/src/gromacs/fileio/mrcdensitymap.h b/src/gromacs/fileio/mrcdensitymap.h
index 7f746567306c96948bce6d7509a65de00c8f9815..aec1d970ac94a26375f37e59c28e8f79e4dd6ecc 100644 (file)
--- a/src/gromacs/fileio/mrcdensitymap.h
+++ b/src/gromacs/fileio/mrcdensitymap.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -46,12 +46,12 @@
 
 #include "gromacs/math/multidimarray.h"
 #include "gromacs/mdspan/extensions.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/classhelpers.h"
 
 namespace gmx
 {
-
+template<typename>
+class ArrayRef;
 struct MrcDensityMapHeader;
 class ISerializer;
 class TranslateAndScale;

diff --git a/src/gromacs/fileio/readinp.cpp b/src/gromacs/fileio/readinp.cpp
index 1d2d5017603d79de8f762804b0505463a1d718b7..907e49050a7c5fd639115e831a5e4c1bbe8c997f 100644 (file)
--- a/src/gromacs/fileio/readinp.cpp
+++ b/src/gromacs/fileio/readinp.cpp
@@ -45,6 +45,7 @@
 #include <algorithm>
 
 #include "gromacs/fileio/warninp.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/binaryinformation.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"

diff --git a/src/gromacs/fileio/readinp.h b/src/gromacs/fileio/readinp.h
index e8e23f0d17d5453bb9f8c4fe6da868b5487d1cad..4ae78cb21a4a88787523195fa433c7b661915cac 100644 (file)
--- a/src/gromacs/fileio/readinp.h
+++ b/src/gromacs/fileio/readinp.h
@@ -44,7 +44,6 @@
 #include <utility>
 #include <vector>
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 
 struct warninp;
@@ -52,6 +51,8 @@ typedef warninp* warninp_t;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class KeyValueTreeObject;
 class TextInputStream;
 class TextOutputStream;

diff --git a/src/gromacs/fileio/tests/mrcdensitymapheader.cpp b/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
index e9e17df359a87e4d0f267058456ed815e2964cd8..0cc8580d654377e70ba5772e5bb179715ccae5b4 100644 (file)
--- a/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
+++ b/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -50,6 +50,8 @@
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
+#include "gromacs/utility/arrayref.h"
+
 #include "testutils/testasserts.h"
 #include "testutils/testmatchers.h"
 

diff --git a/src/gromacs/fileio/tngio.h b/src/gromacs/fileio/tngio.h
index 1ee34cc1406ddba47f2ad3c2799b05ff961a416e..6a33e33d9699695c6c65537783220aa19fe5ad38 100644 (file)
--- a/src/gromacs/fileio/tngio.h
+++ b/src/gromacs/fileio/tngio.h
@@ -40,7 +40,6 @@
 #include <cstdio>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
@@ -50,6 +49,11 @@ struct gmx_tng_trajectory;
 typedef struct gmx_tng_trajectory* gmx_tng_trajectory_t;
 struct t_trxframe;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
 /*! \brief Open a TNG trajectory file
  *
  * \param filename   Name of file to open

diff --git a/src/gromacs/fileio/tpxio.h b/src/gromacs/fileio/tpxio.h
index b3633a7c792522272fade48177b8430095c4f896..5fc0bea2bce3b675c67b49982c45d42d541fb849 100644 (file)
--- a/src/gromacs/fileio/tpxio.h
+++ b/src/gromacs/fileio/tpxio.h
@@ -44,7 +44,6 @@
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
@@ -55,6 +54,11 @@ struct t_inputrec;
 class t_state;
 struct t_topology;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
 /*! \libinternal
  * \brief
  * First part of the TPR file structure containing information about

diff --git a/src/gromacs/fileio/trxio.h b/src/gromacs/fileio/trxio.h
index 8940bc5903027568551415478dfbb5eb4544c819..ae1660c99ac33d13a573fa019f278b227183fba3 100644 (file)
--- a/src/gromacs/fileio/trxio.h
+++ b/src/gromacs/fileio/trxio.h
@@ -40,7 +40,6 @@
 #define GMX_FILEIO_TRXIO_H
 
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/utility/arrayref.h"
 
 struct gmx_mtop_t;
 struct gmx_output_env_t;
@@ -49,6 +48,11 @@ struct t_fileio;
 struct t_topology;
 struct t_trxframe;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
 /* a dedicated status type contains fp, etc. */
 typedef struct t_trxstatus t_trxstatus;
 

diff --git a/src/gromacs/gmxana/powerspect.cpp b/src/gromacs/gmxana/powerspect.cpp
index c8cbfa896337852b0445b4c3030669ed69411710..118491ccf12a3c0c876179a98c24c804389b6cc0 100644 (file)
--- a/src/gromacs/gmxana/powerspect.cpp
+++ b/src/gromacs/gmxana/powerspect.cpp
@@ -40,6 +40,7 @@
 
 #include "gromacs/fft/fft.h"
 #include "gromacs/gmxana/interf.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/real.h"

diff --git a/src/gromacs/gmxana/powerspect.h b/src/gromacs/gmxana/powerspect.h
index da1c36d91253452ba8dc7f074d27fc3281a09be1..e37bb57c1738b5de697145ea52446722da65fcf5 100644 (file)
--- a/src/gromacs/gmxana/powerspect.h
+++ b/src/gromacs/gmxana/powerspect.h
@@ -41,9 +41,14 @@
 #include <vector>
 
 #include "gromacs/gmxana/interf.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/real.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 extern void powerspectavg(real*** interface, int t, int xbins, int ybins, gmx::ArrayRef<const std::string> outfiles);
 
 extern void powerspectavg_intf(t_interf***                      if1,

diff --git a/src/gromacs/gmxana/tests/entropy.cpp b/src/gromacs/gmxana/tests/entropy.cpp
index ff2ec4de0c3000e19326c06fca59919800a6bd15..2890f084af02254aea7346470b5e5b0fbe1e02c8 100644 (file)
--- a/src/gromacs/gmxana/tests/entropy.cpp
+++ b/src/gromacs/gmxana/tests/entropy.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020, 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.
@@ -41,6 +41,7 @@
 #include "gmxpre.h"
 
 #include "gromacs/gmxana/thermochemistry.h"
+#include "gromacs/utility/arrayref.h"
 
 #include "testutils/refdata.h"
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/gmxana/thermochemistry.h b/src/gromacs/gmxana/thermochemistry.h
index b704d0e8d32dd5ddf67cafe5849a7df312532c75..efc50dd8531791a68117b7a8ede5483f28f1dd40 100644 (file)
--- a/src/gromacs/gmxana/thermochemistry.h
+++ b/src/gromacs/gmxana/thermochemistry.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020, 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.
@@ -43,9 +43,14 @@
 
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /*! \brief Compute zero point energy from an array of eigenvalues.
  *
  * This routine first converts the eigenvalues from a normal mode

diff --git a/src/gromacs/gmxpreprocess/add_par.h b/src/gromacs/gmxpreprocess/add_par.h
index 048d42e799f0a0aae66f49b2a56be9de1a95e659..22d60b8477c9da0832d678f9c193dce7158ae2b0 100644 (file)
--- a/src/gromacs/gmxpreprocess/add_par.h
+++ b/src/gromacs/gmxpreprocess/add_par.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020, 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.
@@ -38,12 +38,17 @@
 #ifndef GMX_GMXPREPROCESS_ADD_PAR_H
 #define GMX_GMXPREPROCESS_ADD_PAR_H
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/real.h"
 
 struct InteractionsOfType;
 struct PreprocessResidue;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s);
 
 void add_cmap_param(InteractionsOfType* ps, int ai, int aj, int ak, int al, int am, const char* s);

diff --git a/src/gromacs/gmxpreprocess/convparm.h b/src/gromacs/gmxpreprocess/convparm.h
index 5268cde9fcbe5094e2485e5343d788c98b1cd2f8..a3d65b8e846219e96e7daf97bb782a0a25581823 100644 (file)
--- a/src/gromacs/gmxpreprocess/convparm.h
+++ b/src/gromacs/gmxpreprocess/convparm.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2020, 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.
@@ -38,13 +38,18 @@
 #ifndef GMX_GMXPREPROCESS_CONVPARM_H
 #define GMX_GMXPREPROCESS_CONVPARM_H
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/real.h"
 
 struct gmx_mtop_t;
 struct MoleculeInformation;
 struct InteractionsOfType;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 void convertInteractionsOfType(int                                      atnr,
                                gmx::ArrayRef<const InteractionsOfType>  nbtypes,
                                gmx::ArrayRef<const MoleculeInformation> mi,

diff --git a/src/gromacs/gmxpreprocess/gen_ad.h b/src/gromacs/gmxpreprocess/gen_ad.h
index f05ffdcf4d440f5d6e7e3d1656a69bf673a69906..e722f6c1eb504cfc4aae633e41060b20a68dc131 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_ad.h
+++ b/src/gromacs/gmxpreprocess/gen_ad.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019,2020, 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.
@@ -38,14 +38,18 @@
 #ifndef GMX_GMXPREPROCESS_GEN_AD_H
 #define GMX_GMXPREPROCESS_GEN_AD_H
 
-#include "gromacs/utility/arrayref.h"
-
 struct t_atoms;
 struct t_excls;
 struct MoleculePatchDatabase;
 struct InteractionsOfType;
 struct PreprocessResidue;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 void gen_pad(t_atoms*                               atoms,
              gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
              gmx::ArrayRef<InteractionsOfType>      plist,

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.h b/src/gromacs/gmxpreprocess/gen_vsite.h
index a86f4f49267803f80eb88b265c00f09af18fcfb8..2cd20ce9adbfe105ad73e5a5d6de9d450a7c836e 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.h
+++ b/src/gromacs/gmxpreprocess/gen_vsite.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020, 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.
@@ -38,8 +38,9 @@
 #ifndef GMX_GMXPREPROCESS_GEN_VSITE_H
 #define GMX_GMXPREPROCESS_GEN_VSITE_H
 
+#include <vector>
+
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/real.h"
 
 class PreprocessingAtomTypes;
@@ -48,6 +49,12 @@ struct InteractionsOfType;
 struct PreprocessResidue;
 struct t_symtab;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /* stuff for pdb2gmx */
 
 void do_vsites(gmx::ArrayRef<const PreprocessResidue> rtpFFDB,

diff --git a/src/gromacs/gmxpreprocess/genhydro.h b/src/gromacs/gmxpreprocess/genhydro.h
index a7c451fb2932deadd07360c5b5c948c9a1044ea1..3193d5709b17c3bbe972f36ea5cf4aff34905e81 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.h
+++ b/src/gromacs/gmxpreprocess/genhydro.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020, 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.
@@ -38,13 +38,20 @@
 #ifndef GMX_GMXPREPROCESS_GENHYDRO_H
 #define GMX_GMXPREPROCESS_GENHYDRO_H
 
+#include <vector>
+
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 
 struct t_atoms;
 struct t_symtab;
 struct MoleculePatchDatabase;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /*! \brief
  * Generate hydrogen atoms and N and C terminal patches.
  *

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.h b/src/gromacs/gmxpreprocess/gpp_atomtype.h
index 2ced59ad2358cc6d71a18cd9b7efe7b331650ac8..3cdcee59bb1f8c4e78a429b50d4f521a7129177d 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.h
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2018,2019,2020, 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.
@@ -48,7 +48,6 @@
 
 #include <cstdio>
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/classhelpers.h"
 #include "gromacs/utility/real.h"
 
@@ -59,6 +58,12 @@ class InteractionOfType;
 struct InteractionsOfType;
 struct t_symtab;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /*! \libinternal \brief
  * Storage of all atom types used during preprocessing of a simulation
  * input.

diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.h b/src/gromacs/gmxpreprocess/gpp_nextnb.h
index 8e640c1bab5060438ad4ac42e9ef9bc3242508c3..2788f1853bc40e45eba40b27734d8f34467eca0c 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.h
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2019,2020, 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.
@@ -38,15 +38,15 @@
 #ifndef GMX_GMXPREPROCESS_GPP_NEXTNB_H
 #define GMX_GMXPREPROCESS_GPP_NEXTNB_H
 
-#include "gromacs/utility/arrayref.h"
-
 struct InteractionsOfType;
 
 namespace gmx
 {
 template<typename>
+class ArrayRef;
+template<typename>
 class ListOfLists;
-}
+} // namespace gmx
 
 struct t_nextnb
 {

diff --git a/src/gromacs/gmxpreprocess/grompp_impl.h b/src/gromacs/gmxpreprocess/grompp_impl.h
index c10d25360af64b60953d3d61706870cdc4a36d9b..47ecb013b4c2f99ed0d5a6a796268c7334b695a4 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp_impl.h
+++ b/src/gromacs/gmxpreprocess/grompp_impl.h
@@ -45,12 +45,17 @@
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/idef.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/listoflists.h"
 #include "gromacs/utility/real.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /*! \libinternal \brief
  * Describes an interaction of a given type, plus its parameters.
  */

diff --git a/src/gromacs/gmxpreprocess/hackblock.cpp b/src/gromacs/gmxpreprocess/hackblock.cpp
index fa74340fee20f65b24119be9c64626cb40b8c8c5..bc00ea2c46f1396e4e569fd68738ff2632991791 100644 (file)
--- a/src/gromacs/gmxpreprocess/hackblock.cpp
+++ b/src/gromacs/gmxpreprocess/hackblock.cpp
@@ -47,6 +47,7 @@
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/symtab.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/hackblock.h b/src/gromacs/gmxpreprocess/hackblock.h
index 9fa36722eb21fde3dbcf4c3b0f8c14400cbf009e..33613291bb5212fd69233d9c59a45ac9fed21251 100644 (file)
--- a/src/gromacs/gmxpreprocess/hackblock.h
+++ b/src/gromacs/gmxpreprocess/hackblock.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020, 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.
@@ -43,15 +43,22 @@
 
 #include <cstdio>
 
+#include <array>
 #include <string>
 #include <vector>
 
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/arrayref.h"
 
 struct t_atom;
 struct t_symtab;
+
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /*! \brief
  * Used for reading .rtp/.tdb
  * ebtsBONDS must be the first, new types can be added to the end

diff --git a/src/gromacs/gmxpreprocess/pdb2top.h b/src/gromacs/gmxpreprocess/pdb2top.h
index 1bd3f2e3e113e38c142d65bdbe58c3510d6e6ac8..b9dd8f8fa4fc59bea9d9df71d8dbf796ea8a6092 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.h
+++ b/src/gromacs/gmxpreprocess/pdb2top.h
@@ -40,17 +40,19 @@
 
 #include <cstdio>
 
+#include <string>
 #include <vector>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 
 class PreprocessingAtomTypes;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class MDLogger;
-}
+} // namespace gmx
 
 struct t_atoms;
 struct t_excls;

diff --git a/src/gromacs/gmxpreprocess/specbond.cpp b/src/gromacs/gmxpreprocess/specbond.cpp
index 9fdf332a270c3743b5139898f1aaca308a3cfad5..5e30f10c28b57b2f4726e2f7a6c7db511177b258 100644 (file)
--- a/src/gromacs/gmxpreprocess/specbond.cpp
+++ b/src/gromacs/gmxpreprocess/specbond.cpp
@@ -48,6 +48,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/gmxpreprocess/pdb2top.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/ter_db.h b/src/gromacs/gmxpreprocess/ter_db.h
index f451c4507476dd8581b31cccdc1ad1cd0adae4c2..25288ce0a308d03e70301919160456b555f4890c 100644 (file)
--- a/src/gromacs/gmxpreprocess/ter_db.h
+++ b/src/gromacs/gmxpreprocess/ter_db.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2018,2019,2020, 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.
@@ -40,11 +40,15 @@
 
 #include <vector>
 
-#include "gromacs/utility/arrayref.h"
-
 class PreprocessingAtomTypes;
 struct MoleculePatchDatabase;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /*! \brief
  * Read database for N&C terminal modifications.
  *

diff --git a/src/gromacs/gmxpreprocess/tomorse.h b/src/gromacs/gmxpreprocess/tomorse.h
index 647279996aa372767e26a70b3d40d5ea96a46b71..e41adeb7145080a4a6ab332657620bab056e00c8 100644 (file)
--- a/src/gromacs/gmxpreprocess/tomorse.h
+++ b/src/gromacs/gmxpreprocess/tomorse.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2020, 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.
@@ -38,11 +38,15 @@
 #ifndef GMX_GMXPREPROCESS_TOMORSE_H
 #define GMX_GMXPREPROCESS_TOMORSE_H
 
-#include "gromacs/utility/arrayref.h"
-
 class PreprocessingAtomTypes;
 struct MoleculeInformation;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 void convert_harmonics(gmx::ArrayRef<MoleculeInformation> mols, PreprocessingAtomTypes* atype);
 
 #endif

diff --git a/src/gromacs/gmxpreprocess/topio.h b/src/gromacs/gmxpreprocess/topio.h
index e42bd306aeace69a790dc6eec75d363090838c64..f39c8ec2f0fe17a100ac8deef983120655ca5dd6 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.h
+++ b/src/gromacs/gmxpreprocess/topio.h
@@ -42,7 +42,6 @@
 #include <memory>
 #include <vector>
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/real.h"
 
 struct gmx_molblock_t;
@@ -58,8 +57,10 @@ typedef warninp* warninp_t;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class MDLogger;
-}
+} // namespace gmx
 
 double check_mol(const gmx_mtop_t* mtop, warninp_t wi);
 /* Check mass and charge */

diff --git a/src/gromacs/gmxpreprocess/toppush.h b/src/gromacs/gmxpreprocess/toppush.h
index 82595099b0904bc483afbb4710e9abfd9bb835bd..66df62b9d303446f36f023f708b54d2063a07cb3 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.h
+++ b/src/gromacs/gmxpreprocess/toppush.h
@@ -41,7 +41,6 @@
 
 #include <vector>
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/real.h"
 
 enum class Directive : int;
@@ -58,6 +57,8 @@ struct warninp;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 struct ExclusionBlock;
 } // namespace gmx
 

diff --git a/src/gromacs/gmxpreprocess/topshake.h b/src/gromacs/gmxpreprocess/topshake.h
index 9244f71df87758d83fe755fc3ec267b3bebc2ef9..93b7bd8e389847d61c716ac8ddb765ca04d16ea9 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.h
+++ b/src/gromacs/gmxpreprocess/topshake.h
@@ -38,15 +38,15 @@
 #ifndef GMX_GMXPREPROCESS_TOPSHAKE_H
 #define GMX_GMXPREPROCESS_TOPSHAKE_H
 
-#include "gromacs/utility/arrayref.h"
-
 struct t_atoms;
 struct InteractionsOfType;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class MDLogger;
-}
+} // namespace gmx
 
 void make_shake(gmx::ArrayRef<InteractionsOfType> plist, t_atoms* atoms, int nshake, const gmx::MDLogger& logger);
 

diff --git a/src/gromacs/gmxpreprocess/toputil.h b/src/gromacs/gmxpreprocess/toputil.h
index 829929bd46e32656ae84ba885843e011698fcc5a..ef1fea15f0758611dd08a47833096dbd15d03e44 100644 (file)
--- a/src/gromacs/gmxpreprocess/toputil.h
+++ b/src/gromacs/gmxpreprocess/toputil.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019,2020, 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.
@@ -40,10 +40,6 @@
 
 #include <cstdio>
 
-#include "gromacs/utility/arrayref.h"
-
-#include "gromacs/utility/arrayref.h"
-
 enum class Directive : int;
 class PreprocessingAtomTypes;
 struct t_atoms;
@@ -53,6 +49,12 @@ struct MoleculeInformation;
 class InteractionOfType;
 struct InteractionsOfType;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /* UTILITIES */
 
 void add_param_to_list(InteractionsOfType* list, const InteractionOfType& b);

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.h b/src/gromacs/gmxpreprocess/vsite_parm.h
index 0141efe4deaac182f24dd9fdca03dd2ed80f5cd3..98d6615114dccc0a5aabaed58b30197c8defb821 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.h
+++ b/src/gromacs/gmxpreprocess/vsite_parm.h
@@ -38,8 +38,6 @@
 #ifndef GMX_GMXPREPROCESS_VSITE_PARM_H
 #define GMX_GMXPREPROCESS_VSITE_PARM_H
 
-#include "gromacs/utility/arrayref.h"
-
 class PreprocessingAtomTypes;
 struct gmx_moltype_t;
 struct t_atoms;
@@ -47,8 +45,10 @@ struct InteractionsOfType;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class MDLogger;
-}
+} // namespace gmx
 
 int set_vsites(bool                              bVerbose,
                t_atoms*                          atoms,

diff --git a/src/gromacs/gmxpreprocess/xlate.h b/src/gromacs/gmxpreprocess/xlate.h
index bb2b12b3755717849126079f4dfffe65d583e478..e37cf210e257b38d5b233e68f2a341c7b4e14dec 100644 (file)
--- a/src/gromacs/gmxpreprocess/xlate.h
+++ b/src/gromacs/gmxpreprocess/xlate.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020, 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.
@@ -38,13 +38,17 @@
 #ifndef GMX_GMXPREPROCESS_XLATE_H
 #define GMX_GMXPREPROCESS_XLATE_H
 
-#include "gromacs/utility/arrayref.h"
-
 class ResidueType;
 struct t_atoms;
 struct PreprocessResidue;
 struct t_symtab;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /* If bResname is true renames atoms based on residue names,
  * otherwise renames atoms based on rtp entry names.
  */

diff --git a/src/gromacs/gpu_utils/tests/devicetransfers.h b/src/gromacs/gpu_utils/tests/devicetransfers.h
index 730f2a1ec6fea28ec137684de107889383c8270a..64acdd5b0ae1caaa7929297d9cc3a047440ae29a 100644 (file)
--- a/src/gromacs/gpu_utils/tests/devicetransfers.h
+++ b/src/gromacs/gpu_utils/tests/devicetransfers.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020, 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.
@@ -51,12 +51,12 @@
 #ifndef GMX_GPU_UTILS_TESTS_DEVICETRANSFERS_H
 #define GMX_GPU_UTILS_TESTS_DEVICETRANSFERS_H
 
-#include "gromacs/utility/arrayref.h"
-
 struct gmx_gpu_info_t;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 
 /*! \brief Helper function for GPU test code to be platform agnostic.
  *

diff --git a/src/gromacs/listed_forces/gpubonded.h b/src/gromacs/listed_forces/gpubonded.h
index 2ad8969019c3839b1455cc29ce33e701d6bcfcfd..1cfeed429d2e92e84a4019d9366ab9361cc81fd7 100644 (file)
--- a/src/gromacs/listed_forces/gpubonded.h
+++ b/src/gromacs/listed_forces/gpubonded.h
@@ -53,7 +53,6 @@
 #include "gromacs/math/vectypes.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/idef.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/classhelpers.h"
 
 class DeviceContext;
@@ -69,6 +68,8 @@ struct gmx_wallcycle;
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
 class StepWorkload;
 
 /*! \brief The number on bonded function types supported on GPUs */

diff --git a/src/gromacs/math/coordinatetransformation.cpp b/src/gromacs/math/coordinatetransformation.cpp
index c380efecf37d5adb108252b31b9ebbef4e3f63a8..e93cdc125eec69dd4372e861e5528fed6b8477dc 100644 (file)
--- a/src/gromacs/math/coordinatetransformation.cpp
+++ b/src/gromacs/math/coordinatetransformation.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -44,6 +44,7 @@
 #include <vector>
 
 #include "gromacs/math/vec.h"
+#include "gromacs/utility/arrayref.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/math/coordinatetransformation.h b/src/gromacs/math/coordinatetransformation.h
index 5e962fc92f7b402767d41473be19d2db90a6eda1..70b74697e23da157dd5b2f1f1906f80836498d06 100644 (file)
--- a/src/gromacs/math/coordinatetransformation.h
+++ b/src/gromacs/math/coordinatetransformation.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -44,12 +44,13 @@
 #define GMX_MATH_COORDINATETRANSFORMATION_H
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/classhelpers.h"
 
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
 class ScaleCoordinates
 {
 public:

diff --git a/src/gromacs/math/gausstransform.h b/src/gromacs/math/gausstransform.h
index c5af105177d7ee710fbaf03002907df25041a79b..40ef38d79024a835d010ec7e9dae2c5fd4d136ea 100644 (file)
--- a/src/gromacs/math/gausstransform.h
+++ b/src/gromacs/math/gausstransform.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -49,13 +49,13 @@
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdspan/extensions.h"
 #include "gromacs/mdspan/mdspan.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/classhelpers.h"
 #include "gromacs/utility/real.h"
 
 namespace gmx
 {
-
+template<typename>
+class ArrayRef;
 /*! \internal
  * \brief Provide result of Gaussian function evaluation on a one-dimensional lattice.
  *

diff --git a/src/gromacs/math/tests/coordinatetransformation.cpp b/src/gromacs/math/tests/coordinatetransformation.cpp
index 28533b42f2ea299b9e066161bc4b958bd4f7775a..5abb0b6f03f7128bf53a043ec5b04e22c5b3727f 100644 (file)
--- a/src/gromacs/math/tests/coordinatetransformation.cpp
+++ b/src/gromacs/math/tests/coordinatetransformation.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -48,6 +48,8 @@
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
+#include "gromacs/utility/arrayref.h"
+
 #include "testutils/testasserts.h"
 #include "testutils/testmatchers.h"
 

diff --git a/src/gromacs/mdlib/boxdeformation.cpp b/src/gromacs/mdlib/boxdeformation.cpp
index b621bb8e5b8e88d4f2534ac37f23226f4af192bf..e42a95fe46d7f15cdce072d993a8e520a6d475d9 100644 (file)
--- a/src/gromacs/mdlib/boxdeformation.cpp
+++ b/src/gromacs/mdlib/boxdeformation.cpp
@@ -58,6 +58,7 @@
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/exceptions.h"
 
 namespace gmx

diff --git a/src/gromacs/mdlib/boxdeformation.h b/src/gromacs/mdlib/boxdeformation.h
index caa863e691a71857f6c3841ba85f5d65e793b406..0eea78a5c28db13393dcdc84677da062b49ee035 100644 (file)
--- a/src/gromacs/mdlib/boxdeformation.h
+++ b/src/gromacs/mdlib/boxdeformation.h
@@ -46,7 +46,6 @@
 #include <memory>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/classhelpers.h"
 #include "gromacs/utility/gmxmpi.h"
@@ -58,6 +57,8 @@ enum class NumRanks;
 namespace gmx
 {
 
+template<typename>
+class ArrayRef;
 class BoxDeformation
 {
 public:

diff --git a/src/gromacs/mdlib/broadcaststructs.h b/src/gromacs/mdlib/broadcaststructs.h
index d6a5b15a264d38a9d9188db5381af12240de9044..f8416edf20f85e9bdd6ca1c91d15d737f49936a8 100644 (file)
--- a/src/gromacs/mdlib/broadcaststructs.h
+++ b/src/gromacs/mdlib/broadcaststructs.h
@@ -48,13 +48,20 @@
 #include <vector>
 
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/utility/arrayref.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/utility/smalloc.h"
 
 struct gmx_mtop_t;
 struct t_inputrec;
 struct PartialDeserializedTprFile;
 class t_state;
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 //! Convenience wrapper for gmx_bcast to communicator of a single value.
 template<typename T>
 void block_bc(MPI_Comm communicator, T& data)

diff --git a/src/gromacs/mdlib/calc_verletbuf.h b/src/gromacs/mdlib/calc_verletbuf.h
index 7314a1bba2de13d1eff4563d47127981d4f1f93a..a013cf2bf9aef0bf49cd541145ebf763b9d23331 100644 (file)
--- a/src/gromacs/mdlib/calc_verletbuf.h
+++ b/src/gromacs/mdlib/calc_verletbuf.h
@@ -37,7 +37,6 @@
 #ifndef GMX_MDLIB_CALC_VERLETBUF_H
 #define GMX_MDLIB_CALC_VERLETBUF_H
 
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
@@ -46,6 +45,8 @@ struct t_inputrec;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class RangePartitioning;
 } // namespace gmx
 

diff --git a/src/gromacs/mdlib/calcmu.cpp b/src/gromacs/mdlib/calcmu.cpp
index 006fe7fffa580f16c8e585707c9b7aa2dd6071de..83a61bed785e557cc689eb8f72a3a03910ad0389 100644 (file)
--- a/src/gromacs/mdlib/calcmu.cpp
+++ b/src/gromacs/mdlib/calcmu.cpp
@@ -47,6 +47,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/utility/arrayref.h"
 
 void calc_mu(int                            start,
              int                            homenr,

diff --git a/src/gromacs/mdlib/calcmu.h b/src/gromacs/mdlib/calcmu.h
index b96f12e86a6d5f995a951945777a837294808dd9..4081afc4efe16a84106468f45035c9a20ced6c20 100644 (file)
--- a/src/gromacs/mdlib/calcmu.h
+++ b/src/gromacs/mdlib/calcmu.h
@@ -41,9 +41,14 @@
 #include <stdio.h>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 void calc_mu(int                            start,
              int                            homenr,
              gmx::ArrayRef<const gmx::RVec> x,

diff --git a/src/gromacs/mdlib/constr.cpp b/src/gromacs/mdlib/constr.cpp
index d832420e9e067a3f2e7c3fd3d267ffc670716b8c..16b5c6eba070c08518a1a1f34ac34631597fe9a4 100644 (file)
--- a/src/gromacs/mdlib/constr.cpp
+++ b/src/gromacs/mdlib/constr.cpp
@@ -76,7 +76,6 @@
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_lookup.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/mdlib/dispersioncorrection.h b/src/gromacs/mdlib/dispersioncorrection.h
index 88c8c7b40b9c2ed409a13711e56d2d29ed8d94b1..ec23aea75c47c1079bfd698e73502eb73758dfed 100644 (file)
--- a/src/gromacs/mdlib/dispersioncorrection.h
+++ b/src/gromacs/mdlib/dispersioncorrection.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, 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.
@@ -40,7 +40,6 @@
 #include <memory>
 
 #include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
 
 struct gmx_mtop_t;
 struct interaction_const_t;
@@ -50,6 +49,8 @@ struct t_inputrec;
 
 namespace gmx
 {
+template<typename>
+class ArrayRef;
 class MDLogger;
 } // namespace gmx
 

diff --git a/src/gromacs/mdlib/ebin.cpp b/src/gromacs/mdlib/ebin.cpp
index a0d0c90fe122e1f9c16ebc23cbe732810a04fbd5..6c830526bea1576778b38cc026603480c4ccdb44 100644 (file)
--- a/src/gromacs/mdlib/ebin.cpp
+++ b/src/gromacs/mdlib/ebin.cpp
@@ -50,6 +50,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/trajectory/energyframe.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/ebin.h b/src/gromacs/mdlib/ebin.h
index d475e37cf02dee68c66ba8d09b2082021120ab1a..ac76a2aade614fcffc7962ec951a2d61cb968ffe 100644 (file)
--- a/src/gromacs/mdlib/ebin.h
+++ b/src/gromacs/mdlib/ebin.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020, 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.
@@ -50,9 +50,14 @@
 
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/trajectory/energyframe.h"
-#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
 /* \brief Running averaging structure ('energy bin') to store thermodynamic values.
  *
  * Collects the data on thermodynamic parameters (energy terms, temperature,

diff --git a/src/gromacs/mdrun/legacymdrunoptions.cpp b/src/gromacs/mdrun/legacymdrunoptions.cpp
index 2b8e3a076021c32ac93f9f7869199fe2e6a2e75e..42d0a7df38148980c1886cf03fa015fa5066e51c 100644 (file)
--- a/src/gromacs/mdrun/legacymdrunoptions.cpp
+++ b/src/gromacs/mdrun/legacymdrunoptions.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011-2019, by the GROMACS development team, led by
+ * Copyright (c) 2011-2019,2020, 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.
@@ -52,6 +52,7 @@
 #include <cstring>
 
 #include "gromacs/math/functions.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/fatalerror.h"
 

diff --git a/src/gromacs/mdrun/runner.h b/src/gromacs/mdrun/runner.h
index 82eccd97d5c83264f9436fac2575b9ced1551d16..13a10041d35e321ef01865432107bd69d92ae372 100644 (file)
--- a/src/gromacs/mdrun/runner.h
+++ b/src/gromacs/mdrun/runner.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018,2019,2020, 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.
@@ -55,6 +55,7 @@
 #include "gromacs/mdrun/mdmodules.h"
 #include "gromacs/mdrunutility/handlerestart.h"
 #include "gromacs/mdtypes/mdrunoptions.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/real.h"