@@ -13,7 +13,7 @@ Changes from version 2.4 which are relevant for users:
...
@@ -13,7 +13,7 @@ Changes from version 2.4 which are relevant for users:
to set correctly the `LD_LIBRARY_PATH` variable for the linux executable to work correctly. The procedure has been tested well on OSX and Linux,
to set correctly the `LD_LIBRARY_PATH` variable for the linux executable to work correctly. The procedure has been tested well on OSX and Linux,
but could give problems on other platform. Please report possible problems on the mailing list.
but could give problems on other platform. Please report possible problems on the mailing list.
-\ref driver now stops correctly when using \ref COMMITTOR. If you want to continue the analysis, use the `NOSTOP` flag in \ref COMMITTOR.
-\ref driver now stops correctly when using \ref COMMITTOR. If you want to continue the analysis, use the `NOSTOP` flag in \ref COMMITTOR.
-\ref METAD the calculation of the reweighting factor is now activated by CALC_RCT instead of REWEIGHTING_NGRID and REWEIGHTING_NHILLS, the frequency of update can be set
-\ref METAD the calculation of the reweighting factor is now activated by CALC_RCT instead of REWEIGHTING_NGRID and REWEIGHTING_NHILLS, the frequency of update can be set
by RCT_USTRIDE, the default value is 1 and should be OK for most of the cases
by RCT_USTRIDE, the default value is 1 and should be OK for most of the cases
- Fixed sign in Cartesian components of \ref PUCKERING with 6 membered rings (thanks to Carol Simoes and Javi Iglesias).
- Fixed sign in Cartesian components of \ref PUCKERING with 6 membered rings (thanks to Carol Simoes and Javi Iglesias).
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@@ -64,7 +64,7 @@ Changes from version 2.4 which are relevant for users:
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@@ -64,7 +64,7 @@ Changes from version 2.4 which are relevant for users:
-\ref SAXS includes the MARTINI bead structure factors for Proteins and Nucleic Acids
-\ref SAXS includes the MARTINI bead structure factors for Proteins and Nucleic Acids
-\ref SAXS includes a GPU implementation based on ArrayFire (need to be linked at compile time) that can be activated with GPU
-\ref SAXS includes a GPU implementation based on ArrayFire (need to be linked at compile time) that can be activated with GPU
-\ref METAINFERENCE and all related methods has a new keyword REGRES_ZERO to scale data using a linear scale fit
-\ref METAINFERENCE and all related methods has a new keyword REGRES_ZERO to scale data using a linear scale fit
-\ref CALIBER new bias to perform Maximum Caliber replica-averaged restrained simulations
-\ref CALIBER new bias to perform Maximum Caliber replica-averaged restrained simulations
- Changes in the eABF/DRR module (contributed by Haochuan Chen and Haohao Fu):
- Changes in the eABF/DRR module (contributed by Haochuan Chen and Haohao Fu):
-\ref DRR now supports the extended generalized ABF(egABF) method.
-\ref DRR now supports the extended generalized ABF(egABF) method.
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@@ -74,7 +74,7 @@ Changes from version 2.4 which are relevant for users:
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@@ -74,7 +74,7 @@ Changes from version 2.4 which are relevant for users:
- Fixed conflicts of output files in multiple replicas.
- Fixed conflicts of output files in multiple replicas.
- Changes in the EDS module:
- Changes in the EDS module:
-\ref EDS implements Levenberg-Marquardt optimization in addition to previous gradient descent.
-\ref EDS implements Levenberg-Marquardt optimization in addition to previous gradient descent.
-\ref EDS no longer automatically increases prefactor for bias parameter updates. This results in more stable optimization for the cases tested.
-\ref EDS no longer automatically increases prefactor for bias parameter updates. This results in more stable optimization for the cases tested.
-\ref EDS now has a larger default RANGE parameter to go with these other changes.
-\ref EDS now has a larger default RANGE parameter to go with these other changes.
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@@ -110,7 +110,7 @@ Changes from version 2.4 which are relevant for developers:
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@@ -110,7 +110,7 @@ Changes from version 2.4 which are relevant for developers:
in the core parts of the code have been eliminated.
in the core parts of the code have been eliminated.
- Exceptions cannot be disabled (`--disable-cxx-exceptions` option has been removed from `./configure`).
- Exceptions cannot be disabled (`--disable-cxx-exceptions` option has been removed from `./configure`).
- Every exception thrown in PLUMED now also writes its message on PLUMED log.
- Every exception thrown in PLUMED now also writes its message on PLUMED log.
- Runtime loader in `Plumed.c` now works also when linked without `-rdynamic` (that is,
- Runtime loader in `Plumed.c` now works also when linked without `-rdynamic` (that is,
its names are not exported). Notice that all the combinations are expected to
its names are not exported). Notice that all the combinations are expected to
work, that is: `Plumed.c` from <=2.4or>=2.5 combined with libplumedKernel
work, that is: `Plumed.c` from <=2.4or>=2.5 combined with libplumedKernel
from <=2.4or>=2.5. In order to achieve this the following changes are implemented:
from <=2.4or>=2.5. In order to achieve this the following changes are implemented:
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@@ -160,7 +160,7 @@ Changes from version 2.4 which are relevant for developers:
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@@ -160,7 +160,7 @@ Changes from version 2.4 which are relevant for developers:
For users:
For users:
- in \ref SAXS the keyword ADDEXP is removed. Furthemore, SAXS intensities are automatically normalised for I(0)=1, in case experimental data are provided, the intensity is rescaled with the intensity of the lowest q provided. As a consequence SCALEINT is only needed for additional adjustments.
- in \ref SAXS the keyword ADDEXP is removed. Furthemore, SAXS intensities are automatically normalised for I(0)=1, in case experimental data are provided, the intensity is rescaled with the intensity of the lowest q provided. As a consequence SCALEINT is only needed for additional adjustments.
- gromacs patch updated to gromacs 2018.5
- gromacs patch updated to gromacs 2018.5
- Fixed a bug in gromacs patch that was resulting in incorrect number of threads (0) set when not explicitly using `-ntomp` on the
- Fixed a bug in gromacs patch that was resulting in incorrect number of threads (0) set when not explicitly using `-ntomp` on the
command line or setting `OMP_NUM_THREADS` (see \issue{446}). To apply this fix you need to re-patch gromacs.
command line or setting `OMP_NUM_THREADS` (see \issue{446}). To apply this fix you need to re-patch gromacs.
Notice that setting the number of threads to zero might lead to inconsistent results when using secondary structure variables
Notice that setting the number of threads to zero might lead to inconsistent results when using secondary structure variables
or other multicolvars.
or other multicolvars.
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@@ -179,9 +179,9 @@ For users:
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@@ -179,9 +179,9 @@ For users:
- Fixed performance of \ref CUSTOM when having zero derivatives with respect to some arguments.
- Fixed performance of \ref CUSTOM when having zero derivatives with respect to some arguments.
- New --parse-only option in \ref driver to check the validity of a plumed input file
- New --parse-only option in \ref driver to check the validity of a plumed input file
- New patch for GROMACS 2019.2
- New patch for GROMACS 2019.2
- Module VES: Fixed performance of \ref BF_CUSTOM for basis functions with linear terms (e.g. having zero derivatives).
- Module VES: Fixed performance of \ref BF_CUSTOM for basis functions with linear terms (e.g. having zero derivatives).
- Python wrappers:
- Python wrappers:
- Python module is now always named `plumed` irrespectively of program prefix and suffix. Notice
- Python module is now always named `plumed` irrespectively of program prefix and suffix. Notice
that python module is installed inside the `lib/program_name` directory and thus it is not necessary to
that python module is installed inside the `lib/program_name` directory and thus it is not necessary to
use `program_name` in order to install multiple modules side by side.
use `program_name` in order to install multiple modules side by side.
- Python module can be compiled without compiling PLUMED first.
- Python module can be compiled without compiling PLUMED first.
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@@ -198,4 +198,4 @@ For users:
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@@ -198,4 +198,4 @@ For users:
- Force using cython when compiling from source. Still using the pre-generated cpp file
- Force using cython when compiling from source. Still using the pre-generated cpp file
when installing from PyPI, to avoid cython dependency.
when installing from PyPI, to avoid cython dependency.
- Using python 2 to create the cpp file uploaded on PyPI (this will change to python 3 in 2.6, see \issue{502}).
- Using python 2 to create the cpp file uploaded on PyPI (this will change to python 3 in 2.6, see \issue{502}).
- Module VES: Fixed a bug in updating of bias potential in VES_LINEAR_EXPANSION that is present for certain integrators that call the calculation of the bias multiple times (see [here](https://groups.google.com/d/msg/plumed-users/kPZu_tNZtgk/LrkS0EqrCQAJ)) and replica exchange.