hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/bias/Bias.h

@@ -0,0 +1,82 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed 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 3 of the License, or
+   (at your option) any later version.
+
+   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_bias_Bias_h
+#define __PLUMED_bias_Bias_h
+
+#include "../core/ActionPilot.h"
+#include "../core/ActionWithValue.h"
+#include "../core/ActionWithArguments.h"
+
+#define PLUMED_BIAS_INIT(ao) Action(ao),Bias(ao)
+
+namespace PLMD {
+namespace bias {
+
+/**
+\ingroup INHERIT
+This is the abstract base class to use for implementing new simulation biases, within it there is
+information as to how to go about implementing a new bias.
+*/
+
+class Bias :
+  public ActionPilot,
+  public ActionWithValue,
+  public ActionWithArguments {
+/// the vector of the forces
+  std::vector<double> outputForces;
+/// the pointer to the bias component
+  Value *valueBias;
+  std::vector<double> accumForces;
+  std::vector<double> forces;
+protected:
+/// set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f
+  void setOutputForce(int i,double force);
+/// set the value of the bias
+  void setBias(double bias);
+public:
+  static void registerKeywords(Keywords&);
+  explicit Bias(const ActionOptions&ao);
+  void apply() override;
+  unsigned getNumberOfDerivatives() override;
+};
+
+inline
+void Bias::setOutputForce(int i,double force) {
+  outputForces[i]=force;
+  valueBias->addDerivative(i,-force);
+}
+
+inline
+void Bias::setBias(double bias) {
+  valueBias->set(bias);
+}
+
+inline
+unsigned Bias::getNumberOfDerivatives() {
+  return getNumberOfArguments();
+}
+
+}
+}
+
+#endif
+

plumed/_lib/include/plumed/bias/ReweightBase.h

@@ -0,0 +1,58 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2016-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed 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 3 of the License, or
+   (at your option) any later version.
+
+   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_bias_ReweightBase_h
+#define __PLUMED_bias_ReweightBase_h
+
+#include "../core/ActionWithValue.h"
+#include "../core/ActionWithArguments.h"
+
+namespace PLMD {
+namespace bias {
+
+class ReweightBase :
+  public ActionWithValue,
+  public ActionWithArguments {
+protected:
+/// The temperature at which you are running the simulation
+  double simtemp;
+public:
+  static void registerKeywords(Keywords&);
+  explicit ReweightBase(const ActionOptions&ao);
+  unsigned getNumberOfDerivatives() override {
+    return 0;
+  }
+  virtual bool buildsWeightStore() const {
+    return false;
+  }
+  void calculate() override;
+  virtual void calculateWeights( const unsigned& nframes ) {}
+  virtual double getLogWeight() = 0;
+  virtual double getWeight( const unsigned& iweight ) const {
+    plumed_error();
+  }
+  virtual void clearData() {}
+  void apply() override {}
+};
+
+}
+}
+#endif

plumed/_lib/include/plumed/blas/blas.h

@@ -0,0 +1,253 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+These files are semi-automatic translations by f2c from the original netlib BLAS library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and
+not the reference BLAS implementation.
+
+The reference BLAS implementation is available from http://www.netlib.org/blas 
+
+BLAS does not come with a formal named "license", but a general statement that 
+
+"The reference BLAS is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to
+our modified BLAS files as the original netlib versions, so do what you want with them.
+However, be warned that we have only tested that they to the right thing in the cases used
+in GROMACS (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_blas_blas_h
+#define __PLUMED_blas_blas_h
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team.
+ * Copyright (c) 2012,2013,2014, 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
+ * Header definitions for the standard BLAS library.
+ *
+ * This is the subset of BLAS routines used for the
+ * linear algebra operations in Gromacs.
+ * Do NOT use this for other purposes - we only provide this as a
+ * simple fallback/reference implementation when no optimized BLAS
+ * is present. If you need an implementation for your own code
+ * there are several much faster versions out there.
+ *
+ * All routines are compatible with the BLAS reference implementation,
+ * meaning they assume fortran-style matrix row/column organization.
+ *
+ * There is plenty of documentation for these routines available
+ * at http://www.netlib.org/blas , so there is no point in repeating
+ * it here.
+ */
+#ifndef GMX_BLAS_H
+#define GMX_BLAS_H
+
+/*! \cond */
+
+
+/* These are not required by this file, but by the internal BLAS
+ * implementation.  In principle, they could be included in each file
+ * that requires them, but this is simpler.  Since the header is internal
+ * to the linearyalgebra/ module, the added complexity may not be worth it. */
+#include "real.h"
+
+#ifndef __PLUMED_BLAS_RETURNS_FLOAT
+#define __PLUMED_BLAS_RETURNS_FLOAT float
+#endif
+#if ! defined (__PLUMED_HAS_EXTERNAL_BLAS)
+#include "def_internal.h"
+namespace PLMD{
+namespace blas{
+#else
+namespace PLMD{
+namespace blas{
+}
+}
+#include "def_external.h"
+extern "C"{
+#endif
+#if 0
+}
+#endif
+
+/* Double precision versions */
+double
+    PLUMED_BLAS_F77_FUNC(dasum, DASUM) (int *n, double *dx, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(daxpy, DAXPY) (int *n, double *da, double *dx, int *incx, double *dy, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(dcopy, DCOPY) (int *n, double *dx, int *incx, double *dy, int *incy);
+
+double
+    PLUMED_BLAS_F77_FUNC(ddot, DDOT) (int *n, double *dx, int *incx, double *dy, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(dgemm, DGEMM) (const char *transa, const char *transb, int *m, int *n, int *k,
+                            double *alpha, double *a, int *lda, double *b, int *ldb,
+                            double *beta, double *c, int *ldc);
+
+void
+    PLUMED_BLAS_F77_FUNC(dgemv, DGEMV) (const char *trans, int *m, int *n, double *alpha, double *a, int *lda,
+                            double *x, int *incx, double *beta, double *y, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(dger, DGER) (int *m, int *n, double *alpha, double *x, int *incx,
+                          double *y, int *incy, double *a, int *lda);
+
+double
+    PLUMED_BLAS_F77_FUNC(dnrm2, DNRM2) (int  *n, double *x, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(drot, DROT) (int *n, double *dx, int *incx,
+                          double *dy, int *incy, double *c, double *s);
+
+void
+    PLUMED_BLAS_F77_FUNC(dscal, DSCAL) (int *n, double *fact, double *dx, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(dswap, DSWAP) (int *n, double *dx, int *incx, double *dy, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(dsymv, DSYMV) (const char *uplo, int *n, double *alpha, double *a, int *lda,
+                            double *x, int *incx, double *beta, double *y, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(dsyr2, DSYR2) (const char *uplo, int *n, double *alpha, double *x, int *incx,
+                            double *y, int *incy, double *a, int *lda);
+
+void
+    PLUMED_BLAS_F77_FUNC(dsyr2k, DSYR2K) (const char *uplo, const char *trans, int *n, int *k, double *alpha, double *a,
+                              int *lda, double *b, int *ldb, double *beta, double *c, int *ldc);
+
+void
+    PLUMED_BLAS_F77_FUNC(dtrmm, DTRMM) (const char *side, const char *uplo, const char *transa, const char *diag, int *m, int *n,
+                            double *alpha, double *a, int *lda, double *b, int *ldb);
+
+void
+    PLUMED_BLAS_F77_FUNC(dtrmv, DTRMV) (const char *uplo, const char *trans, const char *diag, int *n,
+                            double *a, int *lda, double *x, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(dtrsm, DTRSM) (const char *side, const char *uplo, const char *transa, const char *diag, int *m, int *n,
+                            double *alpha, double *a, int *lda, double *b, int *ldb);
+
+int
+    PLUMED_BLAS_F77_FUNC(idamax, IDAMAX) (int *n, double *dx, int *incx);
+
+
+
+/* Single precision versions */
+__PLUMED_BLAS_RETURNS_FLOAT
+    PLUMED_BLAS_F77_FUNC(sasum, SASUM) (int *n, float *dx, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(saxpy, SAXPY) (int *n, float *da, float *dx, int *incx, float *dy, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(scopy, SCOPY) (int *n, float *dx, int *incx, float *dy, int *incy);
+
+__PLUMED_BLAS_RETURNS_FLOAT
+    PLUMED_BLAS_F77_FUNC(sdot, SDOT) (int *n, float *dx, int *incx, float *dy, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(sgemm, SGEMM) (const char *transa, const char *transb, int *m, int *n, int *k,
+                            float *alpha, float *a, int *lda, float *b, int *ldb,
+                            float *beta, float *c, int *ldc);
+
+void
+    PLUMED_BLAS_F77_FUNC(sgemv, SGEMV) (const char *trans, int *m, int *n, float *alpha, float *a, int *lda,
+                            float *x, int *incx, float *beta, float *y, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(sger, SGER) (int *m, int *n, float *alpha, float *x, int *incx,
+                          float *y, int *incy, float *a, int *lda);
+
+__PLUMED_BLAS_RETURNS_FLOAT
+    PLUMED_BLAS_F77_FUNC(snrm2, SNRM2) (int  *n, float *x, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(srot, SROT) (int *n, float *dx, int *incx,
+                          float *dy, int *incy, float *c, float *s);
+
+void
+    PLUMED_BLAS_F77_FUNC(sscal, SSCAL) (int *n, float *fact, float *dx, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(sswap, SSWAP) (int *n, float *dx, int *incx, float *dy, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(ssymv, SSYMV) (const char *uplo, int *n, float *alpha, float *a, int *lda,
+                            float *x, int *incx, float *beta, float *y, int *incy);
+
+void
+    PLUMED_BLAS_F77_FUNC(ssyr2, SSYR2) (const char *uplo, int *n, float *alpha, float *x, int *incx,
+                            float *y, int *incy, float *a, int *lda);
+
+void
+    PLUMED_BLAS_F77_FUNC(ssyr2k, SSYR2K) (const char *uplo, const char *trans, int *n, int *k, float *alpha, float *a,
+                              int *lda, float *b, int *ldb, float *beta, float *c, int *ldc);
+
+void
+    PLUMED_BLAS_F77_FUNC(strmm, STRMM) (const char *side, const char *uplo, const char *transa, const char *diag, int *m, int *n,
+                            float *alpha, float *a, int *lda, float *b, int *ldb);
+
+void
+    PLUMED_BLAS_F77_FUNC(strmv, STRMV) (const char *uplo, const char *trans, const char *diag, int *n,
+                            float *a, int *lda, float *x, int *incx);
+
+void
+    PLUMED_BLAS_F77_FUNC(strsm, STRSM) (const char *side, const char *uplo, const char *transa, const char *diag, int *m, int *n,
+                            float *alpha, float *a, int *lda, float *b, int *ldb);
+
+int
+    PLUMED_BLAS_F77_FUNC(isamax, ISAMAX) (int *n, float *dx, int *incx);
+
+
+}
+#if ! defined (__PLUMED_HAS_EXTERNAL_BLAS)
+}
+#endif
+
+/*! \endcond */
+
+#endif /* GMX_BLAS_H */
+#endif

plumed/_lib/include/plumed/blas/def_external.h

@@ -0,0 +1,61 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+These files are semi-automatic translations by f2c from the original netlib BLAS library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and
+not the reference BLAS implementation.
+
+The reference BLAS implementation is available from http://www.netlib.org/blas 
+
+BLAS does not come with a formal named "license", but a general statement that 
+
+"The reference BLAS is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to
+our modified BLAS files as the original netlib versions, so do what you want with them.
+However, be warned that we have only tested that they to the right thing in the cases used
+in GROMACS (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_blas_def_external_h
+#define __PLUMED_blas_def_external_h
+#define plumed_blas_dasum PLUMED_BLAS_F77_FUNC(dasum,DASUM)
+#define plumed_blas_daxpy PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)
+#define plumed_blas_dcopy PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)
+#define plumed_blas_ddot PLUMED_BLAS_F77_FUNC(ddot,DDOT)
+#define plumed_blas_dgemm PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)
+#define plumed_blas_dgemv PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)
+#define plumed_blas_dger PLUMED_BLAS_F77_FUNC(dger,DGER)
+#define plumed_blas_dnrm2 PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)
+#define plumed_blas_drot PLUMED_BLAS_F77_FUNC(drot,DROT)
+#define plumed_blas_dscal PLUMED_BLAS_F77_FUNC(dscal,DSCAL)
+#define plumed_blas_dswap PLUMED_BLAS_F77_FUNC(dswap,DSWAP)
+#define plumed_blas_dsymv PLUMED_BLAS_F77_FUNC(dsymv,DSYMV)
+#define plumed_blas_dsyr2 PLUMED_BLAS_F77_FUNC(dsyr2,DSYR2)
+#define plumed_blas_dsyr2k PLUMED_BLAS_F77_FUNC(dsyr2k,DSYR2K)
+#define plumed_blas_dtrmm PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)
+#define plumed_blas_dtrmv PLUMED_BLAS_F77_FUNC(dtrmv,DTRMV)
+#define plumed_blas_dtrsm PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)
+#define plumed_blas_idamax PLUMED_BLAS_F77_FUNC(idamax,IDAMAX)
+#define plumed_blas_sasum PLUMED_BLAS_F77_FUNC(sasum,SASUM)
+#define plumed_blas_saxpy PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)
+#define plumed_blas_scopy PLUMED_BLAS_F77_FUNC(scopy,SCOPY)
+#define plumed_blas_sdot PLUMED_BLAS_F77_FUNC(sdot,SDOT)
+#define plumed_blas_sgemm PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)
+#define plumed_blas_sgemv PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)
+#define plumed_blas_sger PLUMED_BLAS_F77_FUNC(sger,SGER)
+#define plumed_blas_snrm2 PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)
+#define plumed_blas_srot PLUMED_BLAS_F77_FUNC(srot,SROT)
+#define plumed_blas_sscal PLUMED_BLAS_F77_FUNC(sscal,SSCAL)
+#define plumed_blas_sswap PLUMED_BLAS_F77_FUNC(sswap,SSWAP)
+#define plumed_blas_ssymv PLUMED_BLAS_F77_FUNC(ssymv,SSYMV)
+#define plumed_blas_ssyr2 PLUMED_BLAS_F77_FUNC(ssyr2,SSYR2)
+#define plumed_blas_ssyr2k PLUMED_BLAS_F77_FUNC(ssyr2k,SSYR2K)
+#define plumed_blas_strmm PLUMED_BLAS_F77_FUNC(strmm,STRMM)
+#define plumed_blas_strmv PLUMED_BLAS_F77_FUNC(strmv,STRMV)
+#define plumed_blas_strsm PLUMED_BLAS_F77_FUNC(strsm,STRSM)
+#define plumed_blas_isamax PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)
+#endif

plumed/_lib/include/plumed/blas/def_internal.h

@@ -0,0 +1,97 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+These files are semi-automatic translations by f2c from the original netlib BLAS library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and
+not the reference BLAS implementation.
+
+The reference BLAS implementation is available from http://www.netlib.org/blas 
+
+BLAS does not come with a formal named "license", but a general statement that 
+
+"The reference BLAS is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to
+our modified BLAS files as the original netlib versions, so do what you want with them.
+However, be warned that we have only tested that they to the right thing in the cases used
+in GROMACS (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_blas_def_internal_h
+#define __PLUMED_blas_def_internal_h
+/** \ingroup internal-blas */
+#define plumed_blas_dasum PLMD::blas::PLUMED_BLAS_F77_FUNC(dasum,DASUM)
+/** \ingroup internal-blas */
+#define plumed_blas_daxpy PLMD::blas::PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)
+/** \ingroup internal-blas */
+#define plumed_blas_dcopy PLMD::blas::PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)
+/** \ingroup internal-blas */
+#define plumed_blas_ddot PLMD::blas::PLUMED_BLAS_F77_FUNC(ddot,DDOT)
+/** \ingroup internal-blas */
+#define plumed_blas_dgemm PLMD::blas::PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)
+/** \ingroup internal-blas */
+#define plumed_blas_dgemv PLMD::blas::PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)
+/** \ingroup internal-blas */
+#define plumed_blas_dger PLMD::blas::PLUMED_BLAS_F77_FUNC(dger,DGER)
+/** \ingroup internal-blas */
+#define plumed_blas_dnrm2 PLMD::blas::PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)
+/** \ingroup internal-blas */
+#define plumed_blas_drot PLMD::blas::PLUMED_BLAS_F77_FUNC(drot,DROT)
+/** \ingroup internal-blas */
+#define plumed_blas_dscal PLMD::blas::PLUMED_BLAS_F77_FUNC(dscal,DSCAL)
+/** \ingroup internal-blas */
+#define plumed_blas_dswap PLMD::blas::PLUMED_BLAS_F77_FUNC(dswap,DSWAP)
+/** \ingroup internal-blas */
+#define plumed_blas_dsymv PLMD::blas::PLUMED_BLAS_F77_FUNC(dsymv,DSYMV)
+/** \ingroup internal-blas */
+#define plumed_blas_dsyr2 PLMD::blas::PLUMED_BLAS_F77_FUNC(dsyr2,DSYR2)
+/** \ingroup internal-blas */
+#define plumed_blas_dsyr2k PLMD::blas::PLUMED_BLAS_F77_FUNC(dsyr2k,DSYR2K)
+/** \ingroup internal-blas */
+#define plumed_blas_dtrmm PLMD::blas::PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)
+/** \ingroup internal-blas */
+#define plumed_blas_dtrmv PLMD::blas::PLUMED_BLAS_F77_FUNC(dtrmv,DTRMV)
+/** \ingroup internal-blas */
+#define plumed_blas_dtrsm PLMD::blas::PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)
+/** \ingroup internal-blas */
+#define plumed_blas_idamax PLMD::blas::PLUMED_BLAS_F77_FUNC(idamax,IDAMAX)
+/** \ingroup internal-blas */
+#define plumed_blas_sasum PLMD::blas::PLUMED_BLAS_F77_FUNC(sasum,SASUM)
+/** \ingroup internal-blas */
+#define plumed_blas_saxpy PLMD::blas::PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)
+/** \ingroup internal-blas */
+#define plumed_blas_scopy PLMD::blas::PLUMED_BLAS_F77_FUNC(scopy,SCOPY)
+/** \ingroup internal-blas */
+#define plumed_blas_sdot PLMD::blas::PLUMED_BLAS_F77_FUNC(sdot,SDOT)
+/** \ingroup internal-blas */
+#define plumed_blas_sgemm PLMD::blas::PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)
+/** \ingroup internal-blas */
+#define plumed_blas_sgemv PLMD::blas::PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)
+/** \ingroup internal-blas */
+#define plumed_blas_sger PLMD::blas::PLUMED_BLAS_F77_FUNC(sger,SGER)
+/** \ingroup internal-blas */
+#define plumed_blas_snrm2 PLMD::blas::PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)
+/** \ingroup internal-blas */
+#define plumed_blas_srot PLMD::blas::PLUMED_BLAS_F77_FUNC(srot,SROT)
+/** \ingroup internal-blas */
+#define plumed_blas_sscal PLMD::blas::PLUMED_BLAS_F77_FUNC(sscal,SSCAL)
+/** \ingroup internal-blas */
+#define plumed_blas_sswap PLMD::blas::PLUMED_BLAS_F77_FUNC(sswap,SSWAP)
+/** \ingroup internal-blas */
+#define plumed_blas_ssymv PLMD::blas::PLUMED_BLAS_F77_FUNC(ssymv,SSYMV)
+/** \ingroup internal-blas */
+#define plumed_blas_ssyr2 PLMD::blas::PLUMED_BLAS_F77_FUNC(ssyr2,SSYR2)
+/** \ingroup internal-blas */
+#define plumed_blas_ssyr2k PLMD::blas::PLUMED_BLAS_F77_FUNC(ssyr2k,SSYR2K)
+/** \ingroup internal-blas */
+#define plumed_blas_strmm PLMD::blas::PLUMED_BLAS_F77_FUNC(strmm,STRMM)
+/** \ingroup internal-blas */
+#define plumed_blas_strmv PLMD::blas::PLUMED_BLAS_F77_FUNC(strmv,STRMV)
+/** \ingroup internal-blas */
+#define plumed_blas_strsm PLMD::blas::PLUMED_BLAS_F77_FUNC(strsm,STRSM)
+/** \ingroup internal-blas */
+#define plumed_blas_isamax PLMD::blas::PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)
+#endif

plumed/_lib/include/plumed/blas/real.h

@@ -0,0 +1,49 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+These files are semi-automatic translations by f2c from the original netlib BLAS library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and
+not the reference BLAS implementation.
+
+The reference BLAS implementation is available from http://www.netlib.org/blas 
+
+BLAS does not come with a formal named "license", but a general statement that 
+
+"The reference BLAS is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to
+our modified BLAS files as the original netlib versions, so do what you want with them.
+However, be warned that we have only tested that they to the right thing in the cases used
+in GROMACS (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_blas_real_h
+#define __PLUMED_blas_real_h
+    /*! \brief Double precision accuracy */
+#define PLUMED_GMX_DOUBLE_EPS   2.2204460492503131e-16
+
+    /*! \brief Maximum double precision value - reduced 1 unit in last digit for MSVC */
+#define PLUMED_GMX_DOUBLE_MAX   1.7976931348623157e+308
+
+    /*! \brief Minimum double precision value */
+#define PLUMED_GMX_DOUBLE_MIN   2.2250738585072014e-308
+
+    /*! \brief Single precision accuracy */
+#define PLUMED_GMX_FLOAT_EPS    1.19209290e-07F
+
+    /*! \brief Maximum single precision value - reduced 1 unit in last digit for MSVC */
+#define PLUMED_GMX_FLOAT_MAX    3.40282346E+38F
+
+    /*! \brief Minimum single precision value */
+#define PLUMED_GMX_FLOAT_MIN    1.175494351E-38F
+
+#if defined(F77_NO_UNDERSCORE)
+#define PLUMED_BLAS_F77_FUNC(lower,upper) lower
+#else
+#define PLUMED_BLAS_F77_FUNC(lower,upper) lower ## _
+#endif
+
+#endif

plumed/_lib/include/plumed/cltools/CLTool.h

@@ -0,0 +1,32 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed 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 3 of the License, or
+   (at your option) any later version.
+
+   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_cltools_CLTool_h
+#define __PLUMED_cltools_CLTool_h
+#include "../core/CLTool.h"
+namespace PLMD {
+namespace cltools {
+// Ideally core/CLTool.h should be moved to this directory and CLTool should stay in namespace PLMD::cltools
+// With this trick, PLMD::CLTool is visible as PLMD::cltools::CLTool
+using PLMD::CLTool;
+}
+}
+#endif