From 801675ab0786b0cfad312cbbcd1ff30d04c34f5b Mon Sep 17 00:00:00 2001 From: Christoph Niethammer Date: Thu, 23 May 2024 09:56:27 +0200 Subject: [PATCH 1/3] Add log output for site parameters when reading xml input configuration Signed-off-by: Christoph Niethammer --- src/molecules/Site.h | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/src/molecules/Site.h b/src/molecules/Site.h index 411d961040..82caa28536 100644 --- a/src/molecules/Site.h +++ b/src/molecules/Site.h @@ -51,16 +51,17 @@ class Site { \endcode */ virtual void readXML(XMLfileUnits& xmlconfig) { - xmlconfig.getNodeValueReduced("coords/x", _r[0]); - xmlconfig.getNodeValueReduced("coords/y", _r[1]); - xmlconfig.getNodeValueReduced("coords/z", _r[2]); - xmlconfig.getNodeValueReduced("mass", _m); - if (!xmlconfig.getNodeValue("@name", _name)) { Log::global_log->error() << "Cannot find site name. Defaulting to type." << std::endl; xmlconfig.getNodeValue("@type", _name); } - + Log::global_log->info() << "Site name: " << _name << std::endl; + xmlconfig.getNodeValueReduced("coords/x", _r[0]); + xmlconfig.getNodeValueReduced("coords/y", _r[1]); + xmlconfig.getNodeValueReduced("coords/z", _r[2]); + Log::global_log->info() << "Site coordinates: (x, y, z) = (" << _r[0] << ", " << _r[1] << ", " << _r[2] << ")" << std::endl; + xmlconfig.getNodeValueReduced("mass", _m); + Log::global_log->info() << "Site mass: " << _m << std::endl; } virtual ~Site() {} @@ -124,9 +125,11 @@ class LJcenter : public Site { */ void readXML(XMLfileUnits& xmlconfig) { Site::readXML(xmlconfig); + Log::global_log->info() << "Site type: Lennard-Jones 12-6" << std::endl; xmlconfig.getNodeValueReduced("epsilon", _epsilon); xmlconfig.getNodeValueReduced("sigma", _sigma); xmlconfig.getNodeValue("shifted", _shiftRequested); + Log::global_log->info() << "Site parameters: epsilon = " << _epsilon << ", sigma: " << _sigma << ", shifted: " << _shiftRequested << std::endl; } /// write to stream @@ -191,7 +194,9 @@ class Charge : public Site { */ void readXML(XMLfileUnits& xmlconfig) { Site::readXML(xmlconfig); + Log::global_log->info() << "Site type: Charge" << std::endl; xmlconfig.getNodeValueReduced("charge", _q); + Log::global_log->info() << "Site parameters: charge = " << _q << std::endl; } /// write to stream @@ -312,6 +317,7 @@ class Dipole : public OrientedSite { */ void readXML(XMLfileUnits& xmlconfig) { Site::readXML(xmlconfig); + Log::global_log->info() << "Site type: Dipole" << std::endl; bool bAngleInput = true; double theta, phi; bAngleInput = bAngleInput && xmlconfig.getNodeValueReduced("dipolemoment/theta", theta); @@ -324,7 +330,9 @@ class Dipole : public OrientedSite { xmlconfig.getNodeValueReduced("dipolemoment/z", _e[2]); normalize_e(); } + Log::global_log->info() << "Site parameters: dipole moment (ex, ey, ez) = (" << _e[0] << ", " << _e[1] << ", " << _e[2] << ")" << std::endl; xmlconfig.getNodeValueReduced("dipolemoment/abs", _abs); + Log::global_log->info() << "Site parameters: dipole moment abs = " << _abs << std::endl; } double absMy() const { return abs(); } /**< get the absolute value of the dipole moment. */ @@ -374,6 +382,7 @@ class Quadrupole : public OrientedSite { */ void readXML(XMLfileUnits& xmlconfig) { Site::readXML(xmlconfig); + Log::global_log->info() << "Site type: Quadrupole" << std::endl; bool bAngleInput = true; double theta, phi; bAngleInput = bAngleInput && xmlconfig.getNodeValueReduced("quadrupolemoment/theta", theta); @@ -386,7 +395,9 @@ class Quadrupole : public OrientedSite { xmlconfig.getNodeValueReduced("quadrupolemoment/z", _e[2]); normalize_e(); } + Log::global_log->info() << "Site parameters: quadrupole moment (ex, ey, ez) = (" << _e[0] << ", " << _e[1] << ", " << _e[2] << ")" << std::endl; xmlconfig.getNodeValueReduced("quadrupolemoment/abs", _abs); + Log::global_log->info() << "Site parameters: quadrupole moment (abs) = " << _abs << std::endl; } double absQ() const { return abs(); } /**< get the absolute value of the quadrupole moment. */ From c516ebae7148071519fb95b4d526951b24845688 Mon Sep 17 00:00:00 2001 From: HomesGH <55833544+HomesGH@users.noreply.github.com> Date: Wed, 22 May 2024 12:23:14 +0200 Subject: [PATCH 2/3] Add whitespace to output --- src/molecules/Component.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/molecules/Component.cpp b/src/molecules/Component.cpp index b15dc79d66..09c657a914 100644 --- a/src/molecules/Component.cpp +++ b/src/molecules/Component.cpp @@ -31,11 +31,11 @@ void Component::readXML(XMLfileUnits& xmlconfig) { Log::global_log->info() << "Reading in component" << std::endl; unsigned int cid = 0; xmlconfig.getNodeValue( "@id", cid ); - Log::global_log->info() << "Component ID:" << cid << std::endl; + Log::global_log->info() << "Component ID: " << cid << std::endl; setID(cid - 1); std::string name; xmlconfig.getNodeValue( "@name", name ); - Log::global_log->info() << "Component name:" << name << std::endl; + Log::global_log->info() << "Component name: " << name << std::endl; setName(name); XMLfile::Query query = xmlconfig.query( "site" ); From 550a15812b0ec2df1b27f9494aedbd461564a846 Mon Sep 17 00:00:00 2001 From: Christoph Niethammer Date: Thu, 23 May 2024 14:57:30 +0200 Subject: [PATCH 3/3] Change log message level related to missing site name from error to warning. Signed-off-by: Christoph Niethammer --- src/molecules/Site.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/molecules/Site.h b/src/molecules/Site.h index 82caa28536..1dc3278538 100644 --- a/src/molecules/Site.h +++ b/src/molecules/Site.h @@ -52,7 +52,7 @@ class Site { */ virtual void readXML(XMLfileUnits& xmlconfig) { if (!xmlconfig.getNodeValue("@name", _name)) { - Log::global_log->error() << "Cannot find site name. Defaulting to type." << std::endl; + Log::global_log->warning() << "Cannot find site name. Defaulting to type." << std::endl; xmlconfig.getNodeValue("@type", _name); } Log::global_log->info() << "Site name: " << _name << std::endl;